qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. -------------------------------------------------------------------------- Open MPI failed to open an OpenFabrics device. This is an unusual error; the system reported the OpenFabrics device as being present, but then later failed to access it successfully. This usually indicates either a misconfiguration or a failed OpenFabrics hardware device. All OpenFabrics support has been disabled in this MPI process; your job may or may not continue. Hostname: n049 Device name: qedr0 Error (9): Bad file descriptor -------------------------------------------------------------------------- qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. qelr_alloc_context: Failed to allocate context for device. [n049][[22753,1],13][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[22753,1],0] [n049][[22753,1],11][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[22753,1],0] [n049][[22753,1],19][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[22753,1],0] [n049][[22753,1],3][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[22753,1],0] [n049][[22753,1],31][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[22753,1],0] [n049][[22753,1],7][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[22753,1],0] [n049][[22753,1],29][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[22753,1],0] [n049][[22753,1],17][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[22753,1],0] [n049][[22753,1],23][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[22753,1],0] [n049][[22753,1],9][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[22753,1],0] [n049][[22753,1],27][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[22753,1],0] [n049][[22753,1],5][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[22753,1],0] [n049][[22753,1],21][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[22753,1],0] [n049][[22753,1],1][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[22753,1],0] [n049][[22753,1],25][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[22753,1],0] [n049][[22753,1],15][btl_openib_proc.c:157:mca_btl_openib_proc_create] [btl_openib_proc.c:157] ompi_modex_recv failed for peer [[22753,1],0] Parameter: CNT <- "1" 1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Free Version 42b2 February 15, 2018 709 Copyright(c) 1984-2014 President and Fellows of Harvard College All Rights Reserved Current operating system: Linux-3.10.0-1160.25.1.el7.x86_64(x86_64)@n049.cl Created on 8/11/21 at 14:09:45 by user: 013293967 Maximum number of ATOMS: 360720, and RESidues: 120240 RDTITL> * GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V2.0 ON DEC, 11. 2018. JOBID=1544572063 RDTITL> * INPUT FILES FOR PRODUCTION RDTITL> * PRODUCTION COMMAND: $CHARMMEXEC CNT=1 < STEP7_PRODUCTION.INP > STEP7_PROUDCTION.OUT RDTITL> * CHARMM> CHARMM> DIMENS CHSIZE 3000000 MAXRES 3000000 Size Original New MAXA 360720 3000000 MAXB 360720 3000000 MAXT 721440 6000000 MAXP 1082160 9000000 MAXIMP 180360 1500000 MAXNB 90180 750000 MAXPAD 360720 3000000 MAXRES 120240 3000000 MAXSEG 45090 375000 MAXATC 1400 MAXCB 3000 MAXCT 50000 MAXCP 20000 MAXCI 1200 MAXCH 6400 MAXCN 502503 MAXCRT 120240 1000000 CHARMM> CHARMM> ! Read topology and parameter files CHARMM> stream toppar.str VOPEN> Attempting to open::toppar.str:: OPNLGU> Unit 99 opened for READONLY access to toppar.str INPUT STREAM SWITCHING TO UNIT 99 RDTITL> * GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V2.0 ON DEC, 11. 2018. JOBID=1544569391 RDTITL> * STREAM FILE FOR TOPOLOGY AND PARAMETER READING RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> ! protein topology and parameter CHARMM> open read card unit 10 name toppar/top_all36_prot.rtf VOPEN> Attempting to open::toppar/top_all36_prot.rtf:: OPNLGU> Unit 10 opened for READONLY access to toppar/top_all36_prot.rtf CHARMM> read rtf card unit 10 MAINIO> Residue topology file being read from unit 10. TITLE> *>>>>>>>>CHARMM36 ALL-HYDROGEN TOPOLOGY FILE FOR PROTEINS <<<<<< TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<< TITLE> *>>>>>>>>>>>>>>>>>>>>>>>>>> MAY 2011 <<<<<<<<<<<<<<<<<<<<<<<<<<<< TITLE> * ALL COMMENTS TO THE CHARMM WEB SITE: WWW.CHARMM.ORG TITLE> * PARAMETER SET DISCUSSION FORUM TITLE> * CHARMM> CHARMM> open read card unit 20 name toppar/par_all36m_prot.prm VOPEN> Attempting to open::toppar/par_all36m_prot.prm:: OPNLGU> Unit 20 opened for READONLY access to toppar/par_all36m_prot.prm CHARMM> read para card unit 20 flex PARAMETER FILE BEING READ FROM UNIT 20 TITLE> *>>>> CHARMM36 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS <<<<<<<<<< TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<<< TITLE> *>>>>>>>>>>>>>>>>>>>>>>>>>> JAN. 2016 <<<<<<<<<<<<<<<<<<<<<<<<<<<< TITLE> * ALL COMMENTS TO THE CHARMM WEB SITE: WWW.CHARMM.ORG TITLE> * PARAMETER SET DISCUSSION FORUM TITLE> * [n049.cluster.com:212050] 50 more processes have sent help message help-ompi-common-verbs.txt / ibv_open_device fail [n049.cluster.com:212050] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> ! nucleic acids CHARMM> open read card unit 10 name toppar/top_all36_na.rtf OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 10 with status "KEEP" VOPEN> Attempting to open::toppar/top_all36_na.rtf:: OPNLGU> Unit 10 opened for READONLY access to toppar/top_all36_na.rtf CHARMM> read rtf card unit 10 append MAINIO> Residue topology file being read from unit 10. TITLE> * \\\\ CHARMM36 ALL-HYDROGEN NUCLEIC ACID TOPOLOGY FILE //// TITLE> * ALEXANDER D. MACKERELL JR. AND COWORKERS TITLE> * APRIL 2011 TITLE> * ALL COMMENTS TO THE CHARMM WEB SITE: WWW.CHARMM.ORG TITLE> * PARAMETER SET DISCUSSION FORUM TITLE> * CHARMM> CHARMM> open read card unit 20 name toppar/par_all36_na.prm OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 20 with status "KEEP" VOPEN> Attempting to open::toppar/par_all36_na.prm:: OPNLGU> Unit 20 opened for READONLY access to toppar/par_all36_na.prm CHARMM> read para card unit 20 append flex PARAMETER FILE BEING READ FROM UNIT 20 TITLE> * \\\\ CHARMM36 ALL-HYDROGEN NUCLEIC ACID PARAMETER FILE //// TITLE> * ALEXANDER D. MACKERELL JR. AND COWORKERS TITLE> * APRIL 2011 TITLE> * ALL COMMENTS TO THE CHARMM WEB SITE: WWW.CHARMM.ORG PARAMETER TITLE> * SET DISCUSSION FORUM TITLE> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> ! carbohydrates CHARMM> open read card unit 10 name toppar/top_all36_carb.rtf OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 10 with status "KEEP" VOPEN> Attempting to open::toppar/top_all36_carb.rtf:: OPNLGU> Unit 10 opened for READONLY access to toppar/top_all36_carb.rtf CHARMM> read rtf card unit 10 append MAINIO> Residue topology file being read from unit 10. TITLE> * $ID: TOP_ALLXX_SUGAR.INP,V 1.106 2014/08/19 19:07:43 ALEX EXP $ TITLE> *>>>>>>>>>>>> ALL-HYDROGEN TOPOLOGIES USED IN THE <<<<<<<<<<<<<<<< TITLE> *>>>>> DEVELOPMENT OF THE CHARMM CARBOHYDRATE FORCE FIELD<<<<<<<< TITLE> *>>>>>>>>>>>>>>>>>>>>>>>>> JUNE 2009 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< TITLE> *>>>>>>>> DIRECT COMMENTS TO ALEXANDER D. MACKERELL JR. <<<<<<<<<< TITLE> *>>>>>>>>>> VIA THE CHARMM WEB SITE: WWW.CHARMM.ORG <<<<<<<<<<<<<< TITLE> *>>>>>>>>>>>>>>> PARAMETER SET DISCUSSION FORUM <<<<<<<<<<<<<<<<<< TITLE> * CHARMM> CHARMM> open read card unit 20 name toppar/par_all36_carb.prm OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 20 with status "KEEP" VOPEN> Attempting to open::toppar/par_all36_carb.prm:: OPNLGU> Unit 20 opened for READONLY access to toppar/par_all36_carb.prm CHARMM> read para card unit 20 append flex PARAMETER FILE BEING READ FROM UNIT 20 TITLE> * $ID: PAR_ALLXX_SUGAR.INP,V 1.132 2014/08/19 19:03:21 ALEX EXP $ TITLE> *>>>>>>>>>>>> ALL-HYDROGEN PARAMETERS USED IN THE <<<<<<<<<<<<<<<< TITLE> *>>>>> DEVELOPMENT OF THE CHARMM CARBOHYDRATE FORCE FIELD<<<<<<<< TITLE> *>>>>>>>>>>>>>>>>>>>>>>>>> JUNE 2009 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< TITLE> *>>>>>>>> DIRECT COMMENTS TO ALEXANDER D. MACKERELL JR. <<<<<<<<<< TITLE> *>>>>>>>>>> VIA THE CHARMM WEB SITE: WWW.CHARMM.ORG <<<<<<<<<<<<<< TITLE> *>>>>>>>>>>>>>>> PARAMETER SET DISCUSSION FORUM <<<<<<<<<<<<<<<<<< TITLE> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> ! lipids CHARMM> open read card unit 10 name toppar/top_all36_lipid.rtf OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 10 with status "KEEP" VOPEN> Attempting to open::toppar/top_all36_lipid.rtf:: OPNLGU> Unit 10 opened for READONLY access to toppar/top_all36_lipid.rtf CHARMM> read rtf card unit 10 append MAINIO> Residue topology file being read from unit 10. TITLE> * \\\\\\\ CHARMM36 ALL-HYDROGEN LIPID TOPOLOGY FILE /////// TITLE> * ALL COMMENTS AND QUESTIONS SHOULD BE SUBMITTED TO THE TITLE> * PARAMETER FORUM AT THE CHARMM WEBSITE: WWW.CHARMM.ORG TITLE> * CHARMM> CHARMM> open read card unit 20 name toppar/par_all36_lipid.prm OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 20 with status "KEEP" VOPEN> Attempting to open::toppar/par_all36_lipid.prm:: OPNLGU> Unit 20 opened for READONLY access to toppar/par_all36_lipid.prm CHARMM> read para card unit 20 append flex PARAMETER FILE BEING READ FROM UNIT 20 TITLE> * \\\\\\\ CHARMM36 ALL-HYDROGEN LIPID PARAMETER FILE /////// TITLE> * ALL COMMENTS AND QUESTIONS SHOULD BE SUBMITTED TO THE TITLE> * PARAMETER FORUM AT THE CHARMM WEBSITE: WWW.CHARMM.ORG TITLE> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> ! CGENFF CHARMM> open read card unit 10 name toppar/top_all36_cgenff.rtf OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 10 with status "KEEP" VOPEN> Attempting to open::toppar/top_all36_cgenff.rtf:: OPNLGU> Unit 10 opened for READONLY access to toppar/top_all36_cgenff.rtf CHARMM> read rtf card unit 10 append MAINIO> Residue topology file being read from unit 10. TITLE> * -------------------------------------------------------------------------- * TITLE> * CGENFF: TOPOLOGY FOR THE CHARMM GENERAL FORCE FIELD V. 4.1 * TITLE> * FOR SMALL MOLECULE DRUG DESIGN * TITLE> * -------------------------------------------------------------------------- * TITLE> * DRUDES PARTICLES WILL BE GENERATED AUTOMATICALLY FOR ALL ATOMS WITH NON-ZERO ALPHA Thole-type dipole screening, Slater-Delta shape {S(u) = 1 - (1+u/2)*exp(-u)}, default radius = 1.300000 WARNING from DECODF -- Zero length string being converted to 0. CHARMM> CHARMM> open read card unit 20 name toppar/par_all36_cgenff.prm OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 20 with status "KEEP" VOPEN> Attempting to open::toppar/par_all36_cgenff.prm:: OPNLGU> Unit 20 opened for READONLY access to toppar/par_all36_cgenff.prm CHARMM> read para card unit 20 append flex PARAMETER FILE BEING READ FROM UNIT 20 TITLE> * -------------------------------------------------------------------------- * TITLE> * CGENFF: PARAMETERS FOR THE CHARMM GENERAL FORCE FIELD V. 4.1 * TITLE> * FOR SMALL MOLECULE DRUG DESIGN * TITLE> * -------------------------------------------------------------------------- * TITLE> * 2017/8: IF PROTEIN, NUCLEIC ACID AND CARBOHYDRATE TOPOLOGY AND PARAMETER FILES TITLE> * ARE NOT READ PRIOR TO THE CGENFF FILES "WARNING: ATOMS IN NBFIX ' errors will TITLE> * BE ENCOUNTERED. THESE CAN BE PASSED BY SETTING BOMLEV ( -2) PRIOR TO READING TITLE> * THIS FILE. IN ADDITION, WHEN GENERATING AROMATIC HALOGENS (CL, BR, I) WITH TITLE> * PRE C41B/C42A VERSIONS OF CHARMM "MISSING PARAMETER" ERRORS WILL BE TITLE> * ENCOUNTERED THAT ALSO REQUIRE SETTING BOMLEV ( -2). TITLE> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> ! Additional topologies and parameters for water and ions CHARMM> stream toppar/toppar_water_ions.str VOPEN> Attempting to open::toppar/toppar_water_ions.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_water_ions.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> * TOPLOGY AND PARAMETER INFORMATION FOR WATER AND IONS. RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> !Testcase CHARMM> !test_water_ions.inp CHARMM> CHARMM> ! IMPORTANT NOTE: this file contains NBFixes between carboxylates and sodium, CHARMM> ! which will only apply if the main files containing carboxylate atom types CHARMM> ! have been read in first! CHARMM> CHARMM> !references CHARMM> ! CHARMM> !TIP3P water model CHARMM> ! CHARMM> !W.L. Jorgensen; J.Chandrasekhar; J.D. Madura; R.W. Impey; CHARMM> !M.L. Klein; "Comparison of simple potential functions for CHARMM> !simulating liquid water", J. Chem. Phys. 79 926-935 (1983). CHARMM> ! CHARMM> !IONS CHARMM> ! CHARMM> !Ions from Roux and coworkers CHARMM> ! CHARMM> !Beglov, D. and Roux, B., Finite Representation of an Infinite CHARMM> !Bulk System: Solvent Boundary Potential for Computer Simulations, CHARMM> !Journal of Chemical Physics, 1994, 100: 9050-9063 CHARMM> ! CHARMM> !ZINC CHARMM> ! CHARMM> !Stote, R.H. and Karplus, M. Zinc Binding in Proteins and CHARMM> !Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: CHARMM> !Structure, Function, and Genetics 23:12-31 (1995) CHARMM> CHARMM> !test "append" to determine if previous toppar files have been read and CHARMM> !add append to "read rtf card" if true CHARMM> set nat ?NATC RDCMND substituted energy or value "?NATC" to "340" Parameter: NAT <- "340" CHARMM> set app Parameter: APP <- "" CHARMM> !We're exploiting what is arguably a bug in the parser. On the left hand side, CHARMM> !the quotes have priority, so NAT is correctly substituted. On the right hand CHARMM> !side, the ? has priority and NATC" (sic) is not a valid substitution... CHARMM> if "@NAT" ne "?NATC" if @nat ne 0 set app append Parameter: NAT -> "340" Parameter: NAT -> "340" RDCMND: can not substitute energy "?NATC"" Comparing ""340"" and ""?NATC"". IF test evaluated as true. Performing command Comparing "340" and "0". IF test evaluated as true. Performing command Parameter: APP <- "APPEND" CHARMM> CHARMM> read rtf card @app Parameter: APP -> "APPEND" MAINIO> Residue topology file being read from unit 98. RDTITL> * TOPOLOGY FOR WATER AND IONS RDTITL> * CHARMM> CHARMM> read para card flex @app Parameter: APP -> "APPEND" PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * PARAMETERS FOR WATER AND IONS RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> ! The following section contains NBFixes for sodium interacting with CHARMM> ! carboxylate oxygens of various CHARMM force fields. It will generate CHARMM> ! level -1 warnings whenever any of these force fields have not been CHARMM> ! read prior to the current stream file. Since we don't want to force CHARMM> ! the user to always read all the force fields, we're suppressing the CHARMM> ! warnings. The only side effect is that you will have "most severe CHARMM> ! warning was at level 0" at the end of your output. Also note that CHARMM> ! the user is responsible for reading the current file last if they CHARMM> ! want the NBFixes to apply. A more elegant solution would require new CHARMM> ! features to be added to CHARMM. CHARMM> ! parallel fix, to avoid duplicated messages in the log CHARMM> set para Parameter: PARA <- "" CHARMM> if ?NUMNODE gt 1 set para node 0 RDCMND substituted energy or value "?NUMNODE" to "32" Comparing "32" and "1". IF test evaluated as true. Performing command Parameter: PARA <- "NODE 0" CHARMM> CHARMM> set wrn ?WRNLEV RDCMND substituted energy or value "?WRNLEV" to "5" Parameter: WRN <- "5" CHARMM> ! Some versions of CHARMM don't seem to initialize wrnlev... CHARMM> if "@WRN" eq "?WRNLEV" set wrn 5 Parameter: WRN -> "5" RDCMND: can not substitute energy "?WRNLEV"" Comparing ""5"" and ""?WRNLEV"". IF test evaluated as false. Skipping command CHARMM> set bom ?bomlev RDCMND substituted energy or value "?BOMLEV" to "0" Parameter: BOM <- "0" CHARMM> WRNLEV -1 @PARA Parameter: PARA -> "NODE 0" CHARMM> BOMLEV -1 @PARA Parameter: PARA -> "NODE 0" CHARMM> read para card flex append PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * NBFIX BETWEEN CARBOXYLATE AND SODIUM RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> BOMLEV @bom @PARA Parameter: BOM -> "0" Parameter: PARA -> "NODE 0" CHARMM> WRNLEV @wrn @PARA Parameter: WRN -> "5" Parameter: PARA -> "NODE 0" CHARMM> CHARMM> return VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_dum_noble_gases.str VOPEN> Attempting to open::toppar/toppar_dum_noble_gases.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_dum_noble_gases.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> * TOPLOGY AND PARAMETER INFORMATION FOR HELIUM, NEON AND A DUMMY ATOM. RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> !Testcase CHARMM> !test_dum_nobel_gases.inp CHARMM> CHARMM> !test "append" to determine if previous toppar files have been read and CHARMM> !add append to "read rtf card" if true CHARMM> set nat ?NATC RDCMND substituted energy or value "?NATC" to "355" Parameter: NAT <- "355" CHARMM> set app Parameter: APP <- "" CHARMM> !We're exploiting what is arguably a bug in the parser. On the left hand side, CHARMM> !the quotes have proirity, so NAT is correctly substituted. On the right hand CHARMM> !side, the ? has priority and NATC" (sic) is not a valid substitution... CHARMM> if "@NAT" ne "?NATC" if @nat ne 0 set app append Parameter: NAT -> "355" Parameter: NAT -> "355" RDCMND: can not substitute energy "?NATC"" Comparing ""355"" and ""?NATC"". IF test evaluated as true. Performing command Comparing "355" and "0". IF test evaluated as true. Performing command Parameter: APP <- "APPEND" CHARMM> CHARMM> read rtf card @app Parameter: APP -> "APPEND" MAINIO> Residue topology file being read from unit 98. RDTITL> * TOPOLOGY FOR HELIUM, NEON AND A DUMMY ATOM. RDTITL> * CHARMM> CHARMM> read para card flex @app Parameter: APP -> "APPEND" PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * PARAMETERS FOR HELIUM, NEON AND A DUMMY ATOM. RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> return VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> CHARMM> ! Additional topologies and parameters for protein CHARMM> stream toppar/toppar_all36_prot_d_aminoacids.str VOPEN> Attempting to open::toppar/toppar_all36_prot_d_aminoacids.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_prot_d_aminoacids.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> *>>>>>>CHARMM36 ALL-HYDROGEN TOPPAR FILE FOR D-PROTEINS <<<<<<< RDTITL> *>>>>>>>>>>>>>>>>>>>>>>>>>> FEB 2012 <<<<<<<<<<<<<<<<<<<<<<<<<<<< RDTITL> * ALL COMMENTS TO THE CHARMM WEB SITE: WWW.CHARMM.ORG RDTITL> * PARAMETER SET DISCUSSION FORUM RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> !update 2016/2. use directly inverted CMAPs CHARMM> CHARMM> !toppar stream file for D-amino acids. Includes new residue CHARMM> !names, inverted CMAP and additional parameters. CHARMM> CHARMM> !Parent files that have to be read prior to streaming this file CHARMM> !top_all36_prot.rtf CHARMM> !par_all36_prot.prm CHARMM> ! CHARMM> !Testcase CHARMM> !test_all36_d_amino_acid.inp CHARMM> CHARMM> !test "append" to determine if previous toppar files have been read and CHARMM> !add append to "read rtf card" if true CHARMM> set nat ?NATC RDCMND substituted energy or value "?NATC" to "358" Parameter: NAT <- "358" CHARMM> set app Parameter: APP <- "" CHARMM> !We're exploiting what is arguably a bug in the parser. On the left hand side, CHARMM> !the quotes have priority, so NAT is correctly substituted. On the right hand CHARMM> !side, the ? has priority and NATC" (sic) is not a valid substitution... CHARMM> if "@NAT" ne "?NATC" if @nat ne 0 set app append Parameter: NAT -> "358" Parameter: NAT -> "358" RDCMND: can not substitute energy "?NATC"" Comparing ""358"" and ""?NATC"". IF test evaluated as true. Performing command Comparing "358" and "0". IF test evaluated as true. Performing command Parameter: APP <- "APPEND" CHARMM> CHARMM> read rtf card @app Parameter: APP -> "APPEND" MAINIO> Residue topology file being read from unit 98. RDTITL> * TOPOLOGY FOR D- AMINOACIDS RDTITL> * CHARMM> CHARMM> read para card flex @app Parameter: APP -> "APPEND" PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * PARAMETERS FOR D- AMINOACIDS RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_prot_fluoro_alkanes.str VOPEN> Attempting to open::toppar/toppar_all36_prot_fluoro_alkanes.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_prot_fluoro_alkanes.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> * TOPOLOGY AND PARAMETERS FOR FLUORINATED ALKANES. RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> !Parent files that have to be read prior to streaming this file CHARMM> !top_all36_prot.rtf CHARMM> !par_all36_prot.prm CHARMM> CHARMM> !Testcase CHARMM> !test_all36_prot_fluoro_alkanes.inp CHARMM> CHARMM> !Reference CHARMM> !Chen, I.-J., Yin, D. and MacKerell, Jr., A.D., "Combined Ab CHARMM> !initio/Empirical Approach for Optimization of Lennard-Jones Parameters CHARMM> !for Polar-Neutral Compounds," Journal of Computational Chemistry, CHARMM> !2002, 23:199-213. CHARMM> ! CHARMM> !Note that these parameters are higly optimized to reproduce the CHARMM> !corresponding condensed phase properties and have not been incorporated CHARMM> !into the CHARMM22 or CHARMM27 biomolecular force fields CHARMM> CHARMM> read rtf card append MAINIO> Residue topology file being read from unit 98. RDTITL> * TOPOLOGY FOR FLUOROALKANES RDTITL> * *** WARNING **** residue ETHA already exists (old one deleted) RESI ETHA 0.0 *** WARNING **** residue FETH already exists (old one deleted) RESI FETH 0.0 *** WARNING **** residue DFET already exists (old one deleted) RESI DFET 0.0 *** WARNING **** residue TFET already exists (old one deleted) RESI TFET 0.0 *** WARNING **** residue TFE already exists (old one deleted) RESI TFE 0.0 There were 5 warning(s) from RTFRDR. CHARMM> CHARMM> read para card flex append PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * FLUOROALKANE PARAMETERS RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> return VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_prot_heme.str VOPEN> Attempting to open::toppar/toppar_all36_prot_heme.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_prot_heme.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> * TOPOLOGY AND PARAMETER STREAM FILE FOR HEME AND RELATED RDTITL> * LIGANDS AND PATCHES. RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> !updated 2016/2, allow for use of AUTOGENERATE ANGLE DIHEDRAl PATCH CHARMM> CHARMM> !Parent files that have to be read prior to streaming this file CHARMM> !top_all36_prot.rtf CHARMM> !par_all36_prot.prm CHARMM> CHARMM> !Testcase CHARMM> !test_all36_prot_heme.inp CHARMM> CHARMM> read rtf card append MAINIO> Residue topology file being read from unit 98. RDTITL> * TOPOLOGY FOR HEME AND RELATED COMPOUNDS AND PATCHES RDTITL> * *** WARNING **** residue CO2 already exists (old one deleted) RESI CO2 0.00 *** WARNING **** residue MES1 already exists (old one deleted) RESI MES1 -1.00 There were 2 warning(s) from RTFRDR. CHARMM> CHARMM> read para card flex append PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * ADDITIONAL PARAMETERS FOR HEME RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> return VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_prot_na_combined.str VOPEN> Attempting to open::toppar/toppar_all36_prot_na_combined.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_prot_na_combined.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> * TOPOLOGY AND PARAMETER STREAM FILE FOR PATCHES TO CREATE RDTITL> * MODEL COMPOUNDS AND PATCHES THAT REQUIRE BOTH PROTEIN AND RDTITL> * NUCLEIC ACID TOPOLOGY AND PARAMETER INFORMATION RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> !Parent files that have to be read prior to streaming this file CHARMM> !top_all36_prot.rtf CHARMM> !par_all36_prot.prm CHARMM> !top_all36_na.rtf CHARMM> !par_all36_na.prm CHARMM> !stream/toppar_all36_prot_fluoro_alkanes.str ! atom types an parameters for fluorinated compounds CHARMM> CHARMM> !Testcase CHARMM> !test_all36_prot_na_combined.inp CHARMM> CHARMM> !all patches must be followed by AUTOGENERATE ANGLES DIHEDRALS CHARMM> CHARMM> !PHOSPHOTYROSINE CHARMM> ! CHARMM> !Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D. and Lim, C. CHARMM> !Structural Characterization of the Phosphotyrosine Binding Region of a CHARMM> !High-Affinity aSH2 Domain-Phosphopeptide Complex by Molecular Dynamics CHARMM> !Simulation and Chemical Shift Calculations. Journal of the American CHARMM> !Chemical Society, 1996, 118: 11265-11277. CHARMM> CHARMM> read rtf card append MAINIO> Residue topology file being read from unit 98. RDTITL> * TOPOLOGY FOR PHOSPHORYLATED AMINO ACIDS RDTITL> * *** WARNING **** residue THFI already exists (old one deleted) RESI THFI 0.00 *** WARNING **** residue THMI already exists (old one deleted) RESI THMI 0.00 *** WARNING **** residue THFA already exists (old one deleted) RESI THFA 0.00 *** WARNING **** residue THAO already exists (old one deleted) RESI THAO 0.00 *** WARNING **** residue RNUS already exists (old one deleted) RESI RNUS 0.00 *** WARNING **** residue NUCL already exists (old one deleted) RESI NUCL -1.00 *** WARNING **** residue PPH1 already exists (old one deleted) RESI PPH1 -1.00 *** WARNING **** residue BMPH already exists (old one deleted) RESI BMPH -1.00 *** WARNING **** residue BMPD already exists (old one deleted) RESI BMPD -2.00 *** WARNING **** residue BDFP already exists (old one deleted) RESI BDFP -1.00 *** WARNING **** residue BDFD already exists (old one deleted) RESI BDFD -2.00 *** WARNING **** residue EP_2 already exists (old one deleted) RESI EP_2 -2.00 *** WARNING **** residue IP_2 already exists (old one deleted) RESI IP_2 -2.00 There were 13 warning(s) from RTFRDR. CHARMM> CHARMM> read para card flex append PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * ADDITIONAL PARAMETERS FOR PHOSPHORYLATED AMINO ACIDS RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_prot_retinol.str VOPEN> Attempting to open::toppar/toppar_all36_prot_retinol.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_prot_retinol.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> * TOPPAR STREAM FILE FOR RETINOL AND RETINAL PARAMETERS RDTITL> * A. LOCCISANO, A.M.W., J. EVANSECK AND A.D. MACKERELL, JR. RDTITL> * APRIL, 2005 RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> !use with c36 protein force fields CHARMM> !top_all36_prot.rtf CHARMM> !par_all36_prot.prm CHARMM> CHARMM> read rtf card append MAINIO> Residue topology file being read from unit 98. RDTITL> * RETINAL/RETINOL AND RELATED MODEL COMPOUNDS RDTITL> * *** WARNING **** residue BTE2 already exists (old one deleted) RESI BTE2 0.00 *** WARNING **** residue 13DB already exists (old one deleted) RESI 13DB 0.00 *** WARNING **** residue 13DP already exists (old one deleted) RESI 13DP 0.00 *** WARNING **** residue DMB1 already exists (old one deleted) RESI DMB1 0.00 *** WARNING **** residue DMP1 already exists (old one deleted) RESI DMP1 0.00 *** WARNING **** residue DMP2 already exists (old one deleted) RESI DMP2 0.00 *** WARNING **** residue CROT already exists (old one deleted) RESI CROT 0.00 *** WARNING **** residue PACP already exists (old one deleted) RESI PACP 0.00 *** WARNING **** residue MECH already exists (old one deleted) RESI MECH 0.00 *** WARNING **** residue TMCH already exists (old one deleted) RESI TMCH 0.00 *** WARNING **** residue FRET already exists (old one deleted) RESI FRET 0.00 *** WARNING **** residue RTOL already exists (old one deleted) RESI RTOL 0.00 *** WARNING **** residue RTAL already exists (old one deleted) RESI RTAL 0.00 *** WARNING **** residue RTAC already exists (old one deleted) RESI RTAC -1.00 *** WARNING **** residue PRAC already exists (old one deleted) RESI PRAC -1.00 *** WARNING **** residue PROL already exists (old one deleted) RESI PROL 0.00 *** WARNING **** residue PRAL already exists (old one deleted) RESI PRAL 0.00 *** WARNING **** residue SCH1 already exists (old one deleted) RESI SCH1 0.00 *** WARNING **** residue SCH2 already exists (old one deleted) RESI SCH2 1.00 *** WARNING **** residue SCH3 already exists (old one deleted) RESI SCH3 1.00 There were 20 warning(s) from RTFRDR. CHARMM> CHARMM> read para card flex append PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * RETINAL/RETINOL AND RELATED PARAMETERS RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> CHARMM> ! Additional topologies and parameters for nucleic acids CHARMM> stream toppar/toppar_all36_na_nad_ppi.str VOPEN> Attempting to open::toppar/toppar_all36_na_nad_ppi.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_na_nad_ppi.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> * CHARMM36 ALL-HYDROGEN NUCLEIC ACID FORCE TOPPAR STREAM FILE RDTITL> * NAD+, NADH, ADP, ATP, PPI AND RELATED ANALOGS RDTITL> * A.D. MACKERELL, JR., JULY 2001 RDTITL> * STREAM FOLLOWING RTF AND PARAM READ OF RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> !Update, 2015/1, nomenclature for NAD+ etc. consistent with PDB CHARMM> CHARMM> !Parent files that have to be read prior to streaming this file CHARMM> !top_all36_na.rtf CHARMM> !par_all36_na.prm CHARMM> CHARMM> !Testcase CHARMM> !test_all36_na_nad_ppi.inp CHARMM> CHARMM> !Reference CHARMM> !Pavelites, J.J., Bash, P.A., Gao, J., and MacKerell, Jr., CHARMM> !A.D. A Molecular Mechanics Force Field for NAD+, NADH and the CHARMM> !Pyrophosphate Groups of Nucleotides, Journal of Computational CHARMM> !Chemistry, 1997, 18: 221-239. CHARMM> CHARMM> read rtf card append MAINIO> Residue topology file being read from unit 98. RDTITL> * NAD, PPI TOPOLOGY RDTITL> * *** WARNING **** residue NIC already exists (old one deleted) RESI NIC 1.00 *** WARNING **** residue NICH already exists (old one deleted) RESI NICH 0.00 *** WARNING **** residue PPI1 already exists (old one deleted) RESI PPI1 -3.00 *** WARNING **** residue PPI2 already exists (old one deleted) RESI PPI2 -2.00 *** WARNING **** residue AMP already exists (old one deleted) RESI AMP -2.00 *** WARNING **** residue ADP already exists (old one deleted) RESI ADP -3.00 *** WARNING **** residue ATP already exists (old one deleted) RESI ATP -4.00 *** WARNING **** residue NAD already exists (old one deleted) RESI NAD -1.00 *** WARNING **** residue NADH already exists (old one deleted) RESI NADH -2.00 *** WARNING **** residue NADP already exists (old one deleted) RESI NADP -2.00 *** WARNING **** residue NDPH already exists (old one deleted) RESI NDPH -3.00 There were 11 warning(s) from RTFRDR. CHARMM> CHARMM> read para card flex append PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * NAD, PPI PARAMETERS RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_na_rna_modified.str VOPEN> Attempting to open::toppar/toppar_all36_na_rna_modified.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_na_rna_modified.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> * ADDITIVE CHARMM FORCE FIELD FOR MODIFIED RIBONUCLEIC ACIDS, INCLUDING RDTITL> * THOSE FOUNDS IN TRNA. YOU XU, KAROLINSKA INSTITUTET, 2015. RDTITL> * | RDTITL> * WARNING: PARAMETERS AND ATOM TYPE ASSIGNMENTS IN THIS FILE ARE SPECIFIC RDTITL> * FOR THESE COMPOUNDS AND SHOULD UNDER NO CIRCUMSTANCES BE APPLIED TO RDTITL> * OTHER ORGANIC MOLECULES RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> ! Xu, Y., Vanommeslaeghe, K., Aleksandrov, A., MacKerell, A.D., CHARMM> ! Jr. Nilsson, L., “Additive CHARMM force field for naturally CHARMM> ! occurring modified ribonucleotides,” Journal of Computational CHARMM> ! Chemistry, DOI: 10.1002/jcc.24307, 2016 CHARMM> CHARMM> ! Should be used with parent files CGenFF: top_all36_cgenff.inp and par_all36_cgenff.inp CHARMM> ! NA36: top_all36_na.inp and par_all36_na.inp CHARMM> ! and Carb36: top_all36_carb.inp and par_all36_carb.inp CHARMM> ! CHARMM> CHARMM> read rtf card append MAINIO> Residue topology file being read from unit 98. RDTITL> * TOPOLOGIES OF MODIFIED NUCLEOTIDES RDTITL> * CHARMM> CHARMM> read param card flex append PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * ADDITIVE CHARMM PARAMETERS FOR MODIFIED NUCLEIC ACIDS, BETA VERSION RDTITL> * YOU XU, KAROLINSKA INSTITUTET, 2015. RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> RETURN VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> CHARMM> ! Additional topologies and parameters for lipids CHARMM> stream toppar/toppar_all36_lipid_bacterial.str VOPEN> Attempting to open::toppar/toppar_all36_lipid_bacterial.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_lipid_bacterial.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> * TOPPAR STREAM FILE FOR BRANCHED AND CYCLIC CHAINED LIPIDS. FOLLOWING READING OF RDTITL> * TOP_ALL36_LIPID.RTF RDTITL> * AND RDTITL> * PAR_ALL36_LIPID.RTF RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> ! REFERENCES CHARMM> ! CHARMM> ! Branched Lipids CHARMM> ! CHARMM> ! Lim, J.B. & Klauda, J.B. Branching at the Iso- and Anteiso- Positions in Complex Chlamydia CHARMM> ! Membranes: A Molecular Dynamics Study. Biochimica et Biophysica Acta (BBA) - Biomembranes CHARMM> ! 1808:323-331 (2011). CHARMM> ! CHARMM> ! Cyclic-replacement of double bond CHARMM> ! CHARMM> ! Pandit, K.R. & Klauda, J.B. Membrane models of E. coli containing cyclic moieties in CHARMM> ! the aliphatic lipid chain. Biochimica et Biophysica Acta (BBA) - Biomembranes CHARMM> ! 1818:1205-1210 (2012). CHARMM> ! CHARMM> CHARMM> set nat ?NATC RDCMND substituted energy or value "?NATC" to "392" Parameter: NAT <- "392" CHARMM> set app Parameter: APP <- "" CHARMM> !We're exploiting what is arguably a bug in the parser. On the left hand side, CHARMM> !the quotes have proirity, so NAT is correctly substituted. On the right hand CHARMM> !side, the ? has priority and NATC" (sic) is not a valid substitution... CHARMM> if "@NAT" ne "?NATC" if @nat ne 0 set app append Parameter: NAT -> "392" Parameter: NAT -> "392" RDCMND: can not substitute energy "?NATC"" Comparing ""392"" and ""?NATC"". IF test evaluated as true. Performing command Comparing "392" and "0". IF test evaluated as true. Performing command Parameter: APP <- "APPEND" CHARMM> CHARMM> read rtf card @app Parameter: APP -> "APPEND" MAINIO> Residue topology file being read from unit 98. RDTITL> * CHOLESTEROL RESIDUES RDTITL> * CHARMM> CHARMM> read para card flex @app Parameter: APP -> "APPEND" PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * NEW PARAMETERS RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> return VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_lipid_cardiolipin.str VOPEN> Attempting to open::toppar/toppar_all36_lipid_cardiolipin.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_lipid_cardiolipin.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> READ RTF CARD APPEND FLEX RDTITL> No title read. Parameter: IN1 <- "" CHARMM> read rtf card append flex MAINIO> Residue topology file being read from unit 98. RDTITL> RDTITL> No title read. WARNING from DECODI -- Zero length string being converted to 0 RTFRDR> WARNING: Version number is NOT specified. CHARMM> CHARMM> return VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_lipid_cholesterol.str VOPEN> Attempting to open::toppar/toppar_all36_lipid_cholesterol.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_lipid_cholesterol.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> * TOPPAR STREAM FILE FOR CHOLESTEROL. STREAM FOLLOWING READING OF RDTITL> * TOP_ALL36_LIPID.RTF RDTITL> * PAR_ALL36_LIPID.RTF RDTITL> * TOP_ALL36_CGENFF.RTF RDTITL> * AND PAR_ALL36_CGENFF.PRM RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> !topology and parameters are included for two cholesterol models. the CHARMM> !model may be selected by setting variable chol_model to 1 or 2, as CHARMM> !specified below CHARMM> ! CHARMM> CHARMM> set chol_model 1 !2 for original Suits et al. model Parameter: CHOL_MODEL <- "1" CHARMM> CHARMM> ! CHARMM> !1) Revised model of Lim et al. This contains a number of NBFIXes that CHARMM> !makes it unsuitable for ANTON (set chol_model 1) CHARMM> ! CHARMM> !2) Original model of Suits et al., which is used on ANTON as well as CHARMM> !being suitable for other systems (set chol_model 2 (or anything but 1....)) CHARMM> ! CHARMM> !references CHARMM> ! CHARMM> !Lim, J.B., Rogaski, B. and Klauda, J.B.. "Update of the Cholesterol Force Field CHARMM> !Parameters in CHARMM" 116: 203-210 (2012). CHARMM> ! CHARMM> !Suits, F., Pitman, M., MacKerell, A.D., Jr., Feller, S.E. "Molecular Level CHARMM> !Organization of Saturated and Polyunsaturated Fatty Acids in a CHARMM> !Phosphatidylcholine Bilayer Containing Cholesterol" Biochemistry, CHARMM> !43(49):15318-28, 2004 CHARMM> ! CHARMM> CHARMM> !test "append" CHARMM> set nat ?NATC RDCMND substituted energy or value "?NATC" to "392" Parameter: NAT <- "392" CHARMM> set app Parameter: APP <- "" CHARMM> !We're exploiting what is arguably a bug in the parser. On the left hand side, CHARMM> !the quotes have priority, so NAT is correctly substituted. On the right hand CHARMM> !side, the ? has priority and NATC" (sic) is not a valid substitution... CHARMM> if "@NAT" ne "?NATC" if @nat ne 0 set app append Parameter: NAT -> "392" Parameter: NAT -> "392" RDCMND: can not substitute energy "?NATC"" Comparing ""392"" and ""?NATC"". IF test evaluated as true. Performing command Comparing "392" and "0". IF test evaluated as true. Performing command Parameter: APP <- "APPEND" CHARMM> CHARMM> if chol_model eq 1 then Comparing "1" and "1". IF test evaluated as true. Performing command CHARMM> CHARMM> ! reference CHARMM> ! Lim, J.B., Rogaski, B. and Klauda, J.B.. "Update of the Cholesterol Force Field CHARMM> ! Parameters in CHARMM" 116: 203-210 (2012). CHARMM> ! CHARMM> CHARMM> read rtf card @app Parameter: APP -> "APPEND" MAINIO> Residue topology file being read from unit 98. RDTITL> * TOPOLOGY FOR CHOLESTEROL RDTITL> * CHARMM> CHARMM> read param card flex @app Parameter: APP -> "APPEND" PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * CHOLESTEROL PARAMETERS RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> return VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_lipid_inositol.str VOPEN> Attempting to open::toppar/toppar_all36_lipid_inositol.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_lipid_inositol.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> READ RTF CARD APPEND RDTITL> No title read. Parameter: IN1 <- "" CHARMM> read rtf card append MAINIO> Residue topology file being read from unit 98. RDTITL> * TOPOLOGY FOR INOSITOL-BASED LIPIDS RDTITL> * CHARMM> CHARMM> RETURN VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_lipid_lps.str VOPEN> Attempting to open::toppar/toppar_all36_lipid_lps.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_lipid_lps.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> READ RTF CARD APPEND RDTITL> No title read. Parameter: IN1 <- "" CHARMM> read rtf card append MAINIO> Residue topology file being read from unit 98. RDTITL> * TOPOLOGY FOR LIPIDA FROM LPS RDTITL> * WARNING from DECODI -- Zero length string being converted to 0 RTFRDR> WARNING: Version number is NOT specified. CHARMM> CHARMM> CHARMM> read param card append flex PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * NEW PARAMETES RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_lipid_miscellaneous.str VOPEN> Attempting to open::toppar/toppar_all36_lipid_miscellaneous.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_lipid_miscellaneous.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> READ RTF CARD APPEND FLEX RDTITL> No title read. Parameter: IN1 <- "" CHARMM> read rtf card append flex MAINIO> Residue topology file being read from unit 98. RDTITL> * TOPOLOGY FOR MISCELLANEOUS LIPIDS RDTITL> * CHARMM> CHARMM> return VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_lipid_model.str VOPEN> Attempting to open::toppar/toppar_all36_lipid_model.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_lipid_model.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> * CHARMM36 ALL-HYDROGEN LIPID FORCE FIELD TOPPAR STREAM FILE RDTITL> * COLLECTION OF RESIDUES AND PATCHES FOR MODEL COMPOUNDS USED RDTITL> * IN THE OPTIMIZATION THE LIPID FORCE FIELD. RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> !Parent files that have to be read prior to streaming this file CHARMM> !top_all36_lipid.rtf CHARMM> !par_all36_lipid.prm CHARMM> CHARMM> !Testcase CHARMM> !test_all36_lipid_model.inp CHARMM> CHARMM> read rtf card append MAINIO> Residue topology file being read from unit 98. RDTITL> * C36 LIPID MODEL COMPOUNDS RDTITL> * *** WARNING **** residue MAS already exists (old one deleted) RESI MAS 0.00 *** WARNING **** residue ETAC already exists (old one deleted) RESI ETAC 0.00 *** WARNING **** residue MPRO already exists (old one deleted) RESI MPRO 0.00 *** WARNING **** residue ACEH already exists (old one deleted) RESI ACEH 0.00 *** WARNING **** residue MP_1 already exists (old one deleted) RESI MP_1 -1.00 *** WARNING **** residue MP_2 already exists (old one deleted) RESI MP_2 -2.00 *** WARNING **** residue MSO4 already exists (old one deleted) RESI MSO4 -1.00 *** WARNING **** residue BUTA already exists (old one deleted) RESI BUTA 0.00 *** WARNING **** residue PENT already exists (old one deleted) RESI PENT 0.00 *** WARNING **** residue HEXA already exists (old one deleted) RESI HEXA 0.00 *** WARNING **** residue ETHE already exists (old one deleted) RESI ETHE 0.00 *** WARNING **** residue PRPE already exists (old one deleted) RESI PRPE 0.00 *** WARNING **** residue BTE1 already exists (old one deleted) RESI BTE1 0.00 *** WARNING **** residue BTE2 already exists (old one deleted) RESI BTE2 0.00 *** WARNING **** residue DIPE already exists (old one deleted) RESI DIPE 0.00 *** WARNING **** residue DIHE already exists (old one deleted) RESI DIHE 0.00 *** WARNING **** residue NC4 already exists (old one deleted) RESI NC4 1.00 *** WARNING **** residue NC5 already exists (old one deleted) RESI NC5 1.00 *** WARNING **** residue CHOL already exists (old one deleted) RESI CHOL 1.00 *** WARNING **** residue ACHO already exists (old one deleted) RESI ACHO 1.00 *** WARNING **** residue PC already exists (old one deleted) RESI PC 0.00 *** WARNING **** residue GPC already exists (old one deleted) RESI GPC 0.00 *** WARNING **** residue TEA already exists (old one deleted) RESI TEA 1.00 *** WARNING **** residue ETAM already exists (old one deleted) RESI ETAM 1.00 *** WARNING **** residue GLYC already exists (old one deleted) RESI GLYC 0.00 *** WARNING **** residue MBUT already exists (old one deleted) RESI MBUT 0.00 There were 26 warning(s) from RTFRDR. CHARMM> CHARMM> return VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_lipid_prot.str VOPEN> Attempting to open::toppar/toppar_all36_lipid_prot.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_lipid_prot.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> * TOPOLOGY AND PARAMETERS FOR LIPID TAIL LINKERS TO CYSTEINE AND GLYCINE, RDTITL> * FOR EXAMPLE, PALMITOYLATION, MARISTOYLATION, FERNASYLATION, GERANYLATION RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> read rtf card append MAINIO> Residue topology file being read from unit 98. RDTITL> * LIPID-MODIFIED PROTEIN RESIDUES RDTITL> * CHARMM> CHARMM> read para card append flex PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * CYSTEIN-PALMITATE PARAMETERS RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> return VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_lipid_pyrophosphate.str VOPEN> Attempting to open::toppar/toppar_all36_lipid_pyrophosphate.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_lipid_pyrophosphate.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> READ RTF CARD APPEND RDTITL> No title read. Parameter: IN1 <- "" CHARMM> read rtf card append MAINIO> Residue topology file being read from unit 98. RDTITL> * TOPOLOGY FOR ACYL PYROPHOSPHATE RDTITL> * CHARMM> CHARMM> read param card flex append PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * PARAMETER FOR ACYL PYROPHOSPHATE RDTITL> *· RDTITL> BONDS PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> RETURN VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_lipid_sphingo.str VOPEN> Attempting to open::toppar/toppar_all36_lipid_sphingo.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_lipid_sphingo.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> * TOPPAR STREAM FOR CERAMIDES AND SPINGOMYELINS; REQUIRES FLEX FORMAT FILES RDTITL> * TOP_ALL36_LIPID.RTF AND PAR_ALL36_LIPID.PRM RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> ! REFERENCES CHARMM> ! CHARMM> ! PSM and SSM Lipids CHARMM> ! CHARMM> ! Venable, R.M., B. Rogaski, H. Rui, A.D. MacKerell, Jr., R.W. Pastor, & J.B. Klauda. CHARMM> ! An Experimentally Validated All-atom Force Field for Sphingomyelin. In prep. (2013). CHARMM> ! CHARMM> ! Ceramide CHARMM> ! CHARMM> ! Submited by Sam Tonddast-Navaei of U. Cincinnati. Advised by Russell Devane CHARMM> ! CHARMM> CHARMM> set nat ?NATC RDCMND substituted energy or value "?NATC" to "392" Parameter: NAT <- "392" CHARMM> set app Parameter: APP <- "" CHARMM> !We're exploiting what is arguably a bug in the parser. On the left hand side, CHARMM> !the quotes have proirity, so NAT is correctly substituted. On the right hand CHARMM> !side, the ? has priority and NATC" (sic) is not a valid substitution... CHARMM> if "@NAT" ne "?NATC" if @nat ne 0 set app append Parameter: NAT -> "392" Parameter: NAT -> "392" RDCMND: can not substitute energy "?NATC"" Comparing ""392"" and ""?NATC"". IF test evaluated as true. Performing command Comparing "392" and "0". IF test evaluated as true. Performing command Parameter: APP <- "APPEND" CHARMM> CHARMM> read rtf card @app Parameter: APP -> "APPEND" MAINIO> Residue topology file being read from unit 98. RDTITL> * CER/SM RESIDUES RDTITL> * CHARMM> CHARMM> read para card flex @app Parameter: APP -> "APPEND" PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * NEW PARAMETERS RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> return VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_lipid_yeast.str VOPEN> Attempting to open::toppar/toppar_all36_lipid_yeast.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_lipid_yeast.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> * TOPPAR STREAM FILE FOR BRANCHED AND CYCLIC CHAINED LIPIDS. FOLLOWING READING OF RDTITL> * TOP_ALL36_LIPID.RTF RDTITL> * AND RDTITL> * PAR_ALL36_LIPID.RTF RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> set nat ?NATC RDCMND substituted energy or value "?NATC" to "396" Parameter: NAT <- "396" CHARMM> set app Parameter: APP <- "" CHARMM> !We're exploiting what is arguably a bug in the parser. On the left hand side, CHARMM> !the quotes have proirity, so NAT is correctly substituted. On the right hand CHARMM> !side, the ? has priority and NATC" (sic) is not a valid substitution... CHARMM> if "@NAT" ne "?NATC" if @nat ne 0 set app append Parameter: NAT -> "396" Parameter: NAT -> "396" RDCMND: can not substitute energy "?NATC"" Comparing ""396"" and ""?NATC"". IF test evaluated as true. Performing command Comparing "396" and "0". IF test evaluated as true. Performing command Parameter: APP <- "APPEND" CHARMM> CHARMM> read rtf card @app Parameter: APP -> "APPEND" MAINIO> Residue topology file being read from unit 98. RDTITL> * CHOLESTEROL RESIDUES RDTITL> * CHARMM> CHARMM> read para card flex @app Parameter: APP -> "APPEND" PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * NEW PARAMETERS RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> return VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_lipid_hmmm.str VOPEN> Attempting to open::toppar/toppar_all36_lipid_hmmm.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_lipid_hmmm.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> READ RTF CARD APPEND FLEX RDTITL> No title read. Parameter: IN1 <- "" CHARMM> read rtf card append flex MAINIO> Residue topology file being read from unit 98. RDTITL> * TOPOLOGY FOR TERMINAL PATCHES FOR HMMM TRUNCATED LIPIDS RDTITL> * WARNING from DECODF -- Zero length string being converted to 0. WARNING from DECODF -- Zero length string being converted to 0. WARNING from DECODF -- Zero length string being converted to 0. WARNING from DECODF -- Zero length string being converted to 0. WARNING from DECODF -- Zero length string being converted to 0. WARNING from DECODF -- Zero length string being converted to 0. WARNING from DECODF -- Zero length string being converted to 0. WARNING from DECODF -- Zero length string being converted to 0. CHARMM> CHARMM> read para card flex @app Parameter: APP -> "APPEND" PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * NEW PARAMETERS RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> return VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_lipid_detergent.str VOPEN> Attempting to open::toppar/toppar_all36_lipid_detergent.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_lipid_detergent.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> * TOPPAR STREAM FILE FOR DETERGENTS AND FATTY ACIDS. RDTITL> * STREAM FOLLOWING READING OF RDTITL> * TOP_ALL36_LIPID.RTF RDTITL> * AND RDTITL> * PAR_ALL36_LIPID.RTF RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> !Additional residues added by Im lab, Aug. 2017 CHARMM> CHARMM> !Fatty acids added Jan. 2016 CHARMM> CHARMM> read rtf card append MAINIO> Residue topology file being read from unit 98. RDTITL> * DETERGENT AND FATTY ACID RESIDUES RDTITL> * CHARMM> CHARMM> read para card append flex PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * SB3-12 AND SB3-14 PARAMETERS RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> return VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> stream toppar/toppar_all36_lipid_ether.str VOPEN> Attempting to open::toppar/toppar_all36_lipid_ether.str:: OPNLGU> Unit 98 opened for READONLY access to toppar/toppar_all36_lipid_ether.str INPUT STREAM SWITCHING TO UNIT 98 RDTITL> * CHARMM36 ALL-HYDROGEN ETHER LIPID FORCE FIELD RDTITL> * ALISON LEONARD (A. L.), 7/18 WITH RICHARD PASTOR AND JEFFERY KLAUDA, JPCB 122(26) PP. 6744 - 6754. RDTITL> Parameter: IN1 <- "" CHARMM> CHARMM> !Parent files that have to be read prior to streaming this file CHARMM> !top_all36_lipid.rtf CHARMM> !par_all36_lipid.prm CHARMM> !top_all36_cgenff.rtf CHARMM> !par_all36_cgenff.prm CHARMM> CHARMM> read rtf card append MAINIO> Residue topology file being read from unit 98. RDTITL> * C36 ETHER MODEL COMPOUNDS RDTITL> * CHARMM> CHARMM> read para card flex append PARAMETER FILE BEING READ FROM UNIT 98 RDTITL> * PARAMETERS RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> return VCLOSE: Closing unit 98 with status "KEEP" RETURNING TO INPUT STREAM 99 CHARMM> CHARMM> ! Additional topologies and parameters for carbohydrates CHARMM> !stream toppar/toppar_all36_carb_glycolipid.str CHARMM> !stream toppar/toppar_all36_carb_glycopeptide.str CHARMM> !stream toppar/toppar_all36_carb_imlab.str CHARMM> CHARMM> ! Additional topologies and parameters for spin/fluorophore labels CHARMM> !stream toppar/toppar_all36_label_spin.str CHARMM> !stream toppar/toppar_all36_label_fluorophore.str CHARMM> CHARMM> CHARMM> ! Custom topology and parameter files for LIG CHARMM> open read card unit 10 name lig/lig_g.rtf OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 10 with status "KEEP" VOPEN> Attempting to open::lig/lig_g.rtf:: OPNLGU> Unit 10 opened for READONLY access to lig/lig_g.rtf CHARMM> read rtf card unit 10 append MAINIO> Residue topology file being read from unit 10. TITLE> * TOPOLOGIES GENERATED BY TITLE> * CHARMM GENERAL FORCE FIELD (CGENFF) PROGRAM VERSION 1.0.0 TITLE> * CHARMM> CHARMM> open read card unit 20 name lig/lig_cmap.prm OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 20 with status "KEEP" VOPEN> Attempting to open::lig/lig_cmap.prm:: OPNLGU> Unit 20 opened for READONLY access to lig/lig_cmap.prm CHARMM> read para flex card unit 20 append PARAMETER FILE BEING READ FROM UNIT 20 TITLE> * PARAMETERS GENERATED BY ANALOGY BY TITLE> * CHARMM GENERAL FORCE FIELD (CGENFF) PROGRAM VERSION 1.0.0 TITLE> * WARNING from DECODI -- Zero length string being converted to 0 PARRDR> WARNING: ATOMS IN PHI1 (CMAP) STOP DONT EXIST PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> VCLOSE: Closing unit 99 with status "KEEP" RETURNING TO INPUT STREAM 5 CHARMM> CHARMM> ! Read the system information CHARMM> stream step6.1_equilibration.str VOPEN> Attempting to open::step6.1_equilibration.str:: OPNLGU> Unit 99 opened for READONLY access to step6.1_equilibration.str INPUT STREAM SWITCHING TO UNIT 99 RDTITL> SET BOXTYPE = RECT RDTITL> No title read. Parameter: IN1 <- "" CHARMM> SET BOXTYPE = RECT Parameter: BOXTYPE <- "RECT" CHARMM> SET XTLTYPE = TETRAGONAL Parameter: XTLTYPE <- "TETRAGONAL" CHARMM> SET A = 68.1127025 Parameter: A <- "68.1127025" CHARMM> SET B = 68.1127025 Parameter: B <- "68.1127025" CHARMM> SET C = 70.182 Parameter: C <- "70.182" CHARMM> SET ALPHA = 90.0 Parameter: ALPHA <- "90.0" CHARMM> SET BETA = 90.0 Parameter: BETA <- "90.0" CHARMM> SET GAMMA = 90.0 Parameter: GAMMA <- "90.0" CHARMM> SET ZCEN = 0.0 Parameter: ZCEN <- "0.0" CHARMM> SET NLIPID = 138 Parameter: NLIPID <- "138" CHARMM> SET NLIPTOP = 69 Parameter: NLIPTOP <- "69" CHARMM> SET NLIPBOT = 69 Parameter: NLIPBOT <- "69" CHARMM> SET NWATER = 3850 Parameter: NWATER <- "3850" CHARMM> SET FFTX = 80 Parameter: FFTX <- "80" CHARMM> SET FFTY = 80 Parameter: FFTY <- "80" CHARMM> SET FFTZ = 80 Parameter: FFTZ <- "80" VCLOSE: Closing unit 99 with status "KEEP" RETURNING TO INPUT STREAM 5 CHARMM> CHARMM> ! Read PSF CHARMM> open read unit 10 card name step5_assembly.psf OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 10 with status "KEEP" VOPEN> Attempting to open::step5_assembly.psf:: OPNLGU> Unit 10 opened for READONLY access to step5_assembly.psf CHARMM> read psf unit 10 card xplor MAINIO> Protein structure file being read from unit 10. ***** LEVEL 1 WARNING FROM ***** ***** Attempting to read XPLOR psf format ****************************************** BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 5 PSFRD2> Reading PSF in the expanded format. TITLE> * GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V2.0 ON DEC, 11. 2018. JOB TITLE> * ASSEMBLE PREVIOUSLY GENERATED COMPONENTS (LIPID BILAYER, PROTEIN, PORE WATER, TITLE> * DATE: 12/11/18 18:53: 7 CREATED BY USER: apache TITLE> * PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 3996 Number of atoms = 30066 Number of groups = 8402 Number of bonds = 29944 Number of angles = 39510 Number of dihedrals = 49954 Number of impropers = 276 Number of cross-terms = 8 Number of HB acceptors = 3850 Number of HB donors = 7700 Number of NB exclusions = 0 Total charge = -0.00000 CHARMM> CHARMM> ! Read Coordinate CHARMM> open read unit 10 card name step5_assembly.crd OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 10 with status "KEEP" VOPEN> Attempting to open::step5_assembly.crd:: OPNLGU> Unit 10 opened for READONLY access to step5_assembly.crd CHARMM> read coor unit 10 card SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V2.0 ON DEC, 11. 2018. JOB TITLE> * ASSEMBLE PREVIOUSLY GENERATED COMPONENTS (LIPID BILAYER, PROTEIN, PORE WATER, TITLE> * DATE: 12/11/18 18:53: 8 CREATED BY USER: APACHE TITLE> * CHARMM> CHARMM> ! CHARMM> ! Previous box information CHARMM> ! CHARMM> CHARMM> calc pcnt = @cnt - 1 Parameter: CNT -> "1" Evaluating: 1-1 Parameter: PCNT <- "0" CHARMM> bomlev -5 MISCOM> Setting BOMLev < -2 is NOT a good idea. CHARMM> if pcnt .eq. 0 open read unit 11 card name step6.6_equilibration.rst Comparing "0" and "0". IF test evaluated as true. Performing command VOPEN> Attempting to open::step6.6_equilibration.rst:: OPNLGU> Unit 11 opened for READONLY access to step6.6_equilibration.rst CHARMM> if pcnt .gt. 0 open read unit 11 card name step7_@pcnt.rst Parameter: PCNT -> "0" Comparing "0" and "0". IF test evaluated as false. Skipping command CHARMM> read coor dynr curr unit 11 SPATIAL COORDINATES BEING READ FROM UNIT 11 TITLE> * GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V2.0 ON DEC, 11. 2018. JOB TITLE> * INPUT FILES FOR EQUILIBRATION TITLE> * DATE: 12/13/18 15:15:16 CREATED BY USER: 013293967 TITLE> * ***** LEVEL 0 WARNING FROM ***** ***** Crystal types do not match ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 READYN> dynamics restart file was read. Current step= 0 READYN> Stored seeds for random number generator ignored. READYN> Maybe restarting from different count of processors. CHARMM> bomlev 0 CHARMM> CHARMM> calc A = ?XTLA RDCMND substituted energy or value "?XTLA" to "64.3836132" Evaluating: 64.3836132 Parameter: A <- "64.3836132" CHARMM> calc B = ?XTLB RDCMND substituted energy or value "?XTLB" to "64.3836132" Evaluating: 64.3836132 Parameter: B <- "64.3836132" CHARMM> calc C = ?XTLC RDCMND substituted energy or value "?XTLC" to "70.0714816" Evaluating: 70.0714816 Parameter: C <- "70.0714816" CHARMM> CHARMM> ! CHARMM> ! Image Setup CHARMM> ! CHARMM> open read unit 10 card name crystal_image.str OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 10 with status "KEEP" VOPEN> Attempting to open::crystal_image.str:: OPNLGU> Unit 10 opened for READONLY access to crystal_image.str CHARMM> CRYSTAL DEFINE @XTLtype @A @B @C @alpha @beta @gamma Parameter: XTLTYPE -> "TETRAGONAL" Parameter: A -> "64.3836132" Parameter: B -> "64.3836132" Parameter: C -> "70.0714816" Parameter: ALPHA -> "90.0" Parameter: BETA -> "90.0" Parameter: GAMMA -> "90.0" Crystal Parameters : Crystal Type = TETR A = 64.38361 B = 64.38361 C = 70.07148 Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 CHARMM> CRYSTAL READ UNIT 10 CARD CRYSTAL FILE BEING READ FROM UNIT 10 TITLE> * GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V2.0 ON DEC, 11. 2018. JOBID=1544572063 TITLE> * STREAM FILE FOR CRYSTAL SYMMETRY OPERATION TITLE> * TITLE> * GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V2.0 ON DEC, 11. 2018. JOB TITLE> * STREAM FILE FOR CRYSTAL SYMMETRY OPERATION TITLE> * THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 26 Transformations have been processed. CHARMM> CHARMM> !Image centering by residue CHARMM> IMAGE BYRESID XCEN 0.0 YCEN 0.0 ZCEN @zcen sele resname TIP3 .or. segid MEMB end Parameter: ZCEN -> "0.0" SELRPN> 29490 atoms have been selected out of 30066 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> CHARMM> ! CHARMM> ! Nonbonded Options CHARMM> ! CHARMM> CHARMM> system "python checkfft.py ?XTLA ?XTLB ?XTLC > checkfft.str" RDCMND substituted energy or value "?XTLA" to "64.3836132" RDCMND substituted energy or value "?XTLB" to "64.3836132" RDCMND substituted energy or value "?XTLC" to "70.0714816" Invoking: python checkfft.py 64.3836132 64.3836132 70.0714816 > checkfft.str CHARMM> stream checkfft.str VOPEN> Attempting to open::checkfft.str:: OPNLGU> Unit 99 opened for READONLY access to checkfft.str INPUT STREAM SWITCHING TO UNIT 99 RDTITL> SET FFTX 72 RDTITL> No title read. Parameter: IN1 <- "" CHARMM> set fftx 72 Parameter: FFTX <- "72" CHARMM> set ffty 72 Parameter: FFTY <- "72" CHARMM> set fftz 80 Parameter: FFTZ <- "80" CHARMM> VCLOSE: Closing unit 99 with status "KEEP" RETURNING TO INPUT STREAM 5 CHARMM> CHARMM> nbonds atom vatom vfswitch bycb - CHARMM> ctonnb 10.0 ctofnb 12.0 cutnb 16.0 cutim 16.0 - CHARMM> inbfrq -1 imgfrq -1 wmin 1.0 cdie eps 1.0 - CHARMM> ewald pmew fftx @fftx ffty @ffty fftz @fftz kappa .34 spline order 6 Parameter: FFTX -> "72" Parameter: FFTY -> "72" Parameter: FFTZ -> "80" SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 RESIDUE 146 OPERATED ON BY TRANSFORMATION C022 RESIDUE 712 OPERATED ON BY TRANSFORMATION C022 RESIDUE 720 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1127 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1137 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1379 OPERATED ON BY TRANSFORMATION C011 RESIDUE 1392 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1420 OPERATED ON BY TRANSFORMATION C010 RESIDUE 1490 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1631 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1758 OPERATED ON BY TRANSFORMATION C016 RESIDUE 1807 OPERATED ON BY TRANSFORMATION C008 RESIDUE 1907 OPERATED ON BY TRANSFORMATION C005 RESIDUE 1987 OPERATED ON BY TRANSFORMATION C010 RESIDUE 2219 OPERATED ON BY TRANSFORMATION C022 RESIDUE 2236 OPERATED ON BY TRANSFORMATION C011 RESIDUE 2547 OPERATED ON BY TRANSFORMATION C016 RESIDUE 2580 OPERATED ON BY TRANSFORMATION C005 RESIDUE 2640 OPERATED ON BY TRANSFORMATION C011 RESIDUE 2653 OPERATED ON BY TRANSFORMATION C011 RESIDUE 2655 OPERATED ON BY TRANSFORMATION C008 RESIDUE 2686 OPERATED ON BY TRANSFORMATION C010 RESIDUE 3004 OPERATED ON BY TRANSFORMATION C005 RESIDUE 3067 OPERATED ON BY TRANSFORMATION C008 RESIDUE 3109 OPERATED ON BY TRANSFORMATION C011 RESIDUE 3216 OPERATED ON BY TRANSFORMATION C005 RESIDUE 3274 OPERATED ON BY TRANSFORMATION C016 RESIDUE 3462 OPERATED ON BY TRANSFORMATION C005 RESIDUE 3581 OPERATED ON BY TRANSFORMATION C022 RESIDUE 3641 OPERATED ON BY TRANSFORMATION C016 RESIDUE 3828 OPERATED ON BY TRANSFORMATION C022 RESIDUE 3834 OPERATED ON BY TRANSFORMATION C005 RESIDUE 3878 OPERATED ON BY TRANSFORMATION C022 RESIDUE 3960 OPERATED ON BY TRANSFORMATION C008 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance -------------------------------------------------------------------------- An MPI process has executed an operation involving a call to the "fork()" system call to create a child process. Open MPI is currently operating in a condition that could result in memory corruption or other system errors; your MPI job may hang, crash, or produce silent data corruption. The use of fork() (or system() or other calls that create child processes) is strongly discouraged. The process that invoked fork was: Local host: n049 (PID 212110) MPI_COMM_WORLD rank: 29 If you are *absolutely sure* that your application will successfully and correctly survive a call to fork(), you may disable this warning by setting the mpi_warn_on_fork MCA parameter to 0. -------------------------------------------------------------------------- 1 C001 has 255 63 59 0.00 2 C002 has 1486 381 358 0.00 3 C003 has 146 46 46 0.48 4 C004 has 1505 407 392 0.00 5 C005 has 7531 1979 1872 0.00 6 C006 has 1383 392 384 0.00 7 C007 has 1957 512 204 0.00 8 C008 has 8850 2403 1030 0.00 9 C009 has 1442 380 168 0.00 10 C010 has 8835 2411 1080 0.00 12 C012 has 211 52 50 0.00 13 C013 has 1502 392 378 0.00 14 C014 has 196 54 53 0.00 Total of65365 atoms and17874 groups and10070 residues were included Total heap storage needed = 1222255 Fill Ewald table: Number of points= 10000 EWXmax= 4.250000 fill erfc table: linear inter has rms error = 0.979220D-08 maximum error = 0.218740D-07 fill erfc table: cubic spline has rms error = 0.360331D-11 maximum error = 0.108438D-10 NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec FSHIft VATOm VFSWIt BYCB NOEXtnd EWALd CUTNB = 16.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 CGONNB = 0.000 CGOFNB = 10.000 WMIN = 1.000 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 PME EWALD OPTIONS: KAPPA = 0.340 QCOR = 0.000 Bspline order = 6 FFTX= 72 FFTY= 72 FFTZ= 80 Using Pub FFT Real-to-Complex FFT There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions. with mode 5 found 65604 exclusions and 49866 interactions(1-4) found 11692 group exclusions. found 0 image group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 0 ATOM PAIRS AND 0 GROUP PAIRS == IMAGES === SPACE FOR 0 ATOM PAIRS AND 0 GROUP PAIRS ========================================= TRIAL run of list........... ========================================= Using Image CUBE search Using Image CUBE search NBNDGCM found: 701027 atom pairs 222633 image atom pairs 0 self atom pairs 19703682 total atom pairs 6943538 total image pairs CHARMM> energy SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 255 63 59 0.00 2 C002 has 1486 381 358 0.00 3 C003 has 146 46 46 0.48 4 C004 has 1505 407 392 0.00 5 C005 has 7531 1979 1872 0.00 6 C006 has 1383 392 384 0.00 7 C007 has 1957 512 204 0.00 8 C008 has 8850 2403 1030 0.00 9 C009 has 1442 380 168 0.00 10 C010 has 8835 2411 1080 0.00 12 C012 has 211 52 50 0.00 13 C013 has 1502 392 378 0.00 14 C014 has 196 54 53 0.00 Total of65365 atoms and17874 groups and10070 residues were included found 0 image group exclusions. NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec FSHIft VATOm VFSWIt BYCB NOEXtnd EWALd CUTNB = 16.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 CGONNB = 0.000 CGOFNB = 10.000 WMIN = 1.000 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 PME EWALD OPTIONS: KAPPA = 0.340 QCOR = 0.000 Bspline order = 6 FFTX= 72 FFTY= 72 FFTZ= 80 Using Pub FFT Real-to-Complex FFT There are 701027 atom pairs and 115470 atom exclusions. There are 0 group pairs and 11692 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 911335 ATOM PAIRS AND 0 GROUP PAIRS == IMAGES === SPACE FOR 289422 ATOM PAIRS AND 0 GROUP PAIRS Using Image CUBE search NBNDGCM found: 701027 atom pairs 222633 image atom pairs 0 self atom pairs 19703682 total atom pairs 6943538 total image pairs ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 22.99 MINUTES CPU TIME: 11.48 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 22.99 MINUTES CPU TIME: 11.48 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 22.94 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 22.94 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 22.94 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 22.94 MINUTES : No cross-term map for 2 ( CG321 HAL2 CTL2 HGA3 ) ( HGA1 HGA3 HGA1 HGA1 ) : No cross-term map for 3 ( HGA2 CG2DC1 HAL2 HGA2 ) ( HGA3 HGA2 HGA3 HGA2 ) : No cross-term map for 4 ( HGA3 HGA3 HGA3 PL ) ( HAL2 PL HAL2 CG321 ) : No cross-term map for 5 ( HGA2 HGA3 HGA2 CTL2 ) ( CTL3 CTL2 CTL3 HGA2 ) : No cross-term map for 6 ( CG321 HAL2 HGA3 HGA2 ) ( CG321 HGA2 HGA3 HGA3 ) : No cross-term map for 7 ( HGA4 CTL2 CTL2 CG321 ) ( CG3C52 CG321 CG3C52 CG3C51 ) : No cross-term map for 8 ( HGA3 HGA3 HAL2 CG2DC2 ) ( CG331 CG2DC2 CG331 HGA3 ) : A TOTAL OF 7 MISSING PARAMETERS ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5 /---------\ / \ / \ / \ ! XXXX XXXX ! ! XXXX XXXX ! ! XXX XXX ! ! X ! --\ XXX /-- ! ! XXX ! ! ! ! ! ! ! I I I I I ! ! I I I I ! \ / -- -- \---/ XXX XXX XXXX XXXX XXXXX XXXXX XXX XXX XXX XXX XXXXX XXX XXX XXX XXX XXX XXX XXXXX XXXXX XXXX XXXX XXX XXX Execution terminated due to the detection of a fatal error. ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 22.94 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 22.94 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 22.94 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 22.94 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 22.94 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 22.94 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 22.94 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 22.94 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 22.94 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 22.94 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 22.94 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 22.94 MINUTES ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 11.48 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 11.48 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 11.47 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 11.48 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 11.48 MINUTES ***** LEVEL -1 WARNING FROM ***** ***** CODES> MISSING PARAMETERS ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 ABNORMAL TERMINATION MOST SEVERE WARNING WAS AT LEVEL -1 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 23.00 MINUTES CPU TIME: 11.47 MINUTES -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[22753,1],0] Exit code: 1 -------------------------------------------------------------------------- [n049.cluster.com:212050] 15 more processes have sent help message help-mpi-runtime.txt / mpi_init:warn-fork