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If I keep the water, I get the same result: SR2 0 0 SS2 0 0 SX2 0 0 SY2 0 0
What is to be done?
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Find the clues in your output file.
Rick Venable computational chemist
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OK, now for the final part, in the output file I get:
ORREL> ! use final mantime to set AVER, FLUC for output CORREL> open write unit 1 card name cd@{C}.txt Parameter: C -> "2" At line 145 of file /home/themis/c39a2/source/util/parse.src (unit = 5, file = 'test.inp') Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::cd2.txt:: OPNLGU> Unit 1 opened for WRITE access to cd2.txt
I think this is the clue, but how do I interpret it?
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The Fortran runtime error message suggests some kind of problem with the file named test.inp; perhaps that file has become corrupted in some way. You have not provided enough information to say any more.
Rick Venable computational chemist
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Here is the file test.inp, for 274 POPC lipids.(I made it following the example above, with a saved trajectory file for lipids without water and a psf file written in charm format.The number of atoms in trajectory file match those in psf ):
! the axial avg order parameter for an input C no. @C ! modified for C=C case; first file @FF last file @LF ! subdir @S
! Read initial data files open unit 1 read form name top_all36_lipid.rtf read rtf card unit 1 close unit 1 open unit 1 read form name par_all36_lipid.prm read param card unit 1 close unit 1
! Read parameter file in command line
open read card unit 1 name popc.psf read psf card unit 1 open read card unit 1 name popc.crd read coor card unit 1
! number of lipids set nl = 274 ! number of files calc n = 1
calc mxa @NL * 6 * 4 calc mxs 10 + @NL*2 * 4 calc mxt 2000 * @N
! unsaturation check; beta chain set ub = 0 define unsat sele atom A 1 C2@C .and. chem CEL1 end if ub lt ?NSEL set ub ?NSEL ! unsaturation check; gamma chain set ug = 0 define unsat sele atom A 1 C3@C .and. chem CEL1 end if ug lt ?NSEL set ug ?NSEL
correl maxtim @MXT maxa @MXA maxs @MXS enter sr zero if ub eq 0 enter ss dupl sr enter sx dupl sr if ug eq 0 enter sy dupl sr set k 1 label elp if ub eq 0 then enter w@K vect z A @K H@{C}R A @K C2@C enter a@K vect r A @K H@{C}R A @K C2@C enter x@K vect z A @K H@{C}S A @K C2@C enter b@K vect r A @K H@{C}S A @K C2@C else enter w@K vect z A @K H@{C}1 A @K C2@C enter a@K vect r A @K H@{C}1 A @K C2@C endif if c gt 15 goto eskip if ug eq 0 then enter y@K vect z A @K H@{C}X A @K C3@C enter c@K vect r A @K H@{C}X A @K C3@C enter z@K vect z A @K H@{C}Y A @K C3@C enter d@K vect r A @K H@{C}Y A @K C3@C else enter y@K vect z A @K H@{C}1 A @K C3@C enter c@K vect r A @K H@{C}1 A @K C3@C endif label eskip incr k by 1 if k le @NL goto elp
! OPEN FILES, FILL SERIES VIA TRAJ
open read unit 1 file name popclipidsnowater.dcd
! LOOP OVER LIPIDS; NORM, CALC SCD, ACCUM set k 1 label clp mantim w@K ratio a@K mantim w@K squa mantim w@K mult 1.5 mantim w@K shift -0.5 mantim sr add w@K if ub eq 0 then mantim x@K ratio b@K mantim x@K squa mantim x@K mult 1.5 mantim x@K shift -0.5 mantim ss add x@K endif if c gt 15 goto mskip mantim y@K ratio c@K mantim y@K squa mantim y@K mult 1.5 mantim y@K shift -0.5 mantim sx add y@K if ug eq 0 then mantim z@K ratio d@K mantim z@K squa mantim z@K mult 1.5 mantim z@K shift -0.5 mantim sy add z@K endif label mskip incr k by 1 if k le @NL goto clp
! use final mantime to set AVER, FLUC for output open write unit 1 card name cd@{C}.txt echu 1 mantim sr divi @NL echo sr@C ?AVER ?FLUC if ub eq 0 then mantim ss divi @NL echo ss@C ?AVER ?FLUC endif if c gt 15 goto oskip mantim sx divi @NL echo sx@C ?AVER ?FLUC if ug eq 0 then mantim sy divi @NL echo sy@C ?AVER ?FLUC endif label oskip close unit 1
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I don't see any problems with the input; however, the error message suggests there are non-printing control characters present in the file. While one possibility for that is accidental file corruption, sometimes this can occur for files which have been edited on a Windows or Mac OS X machine and then transferred to a Linux machine to run CHARMM. Note that TAB characters are not allowed in CHARMM input scripts. You may need to consult with a local computer guru to help you with this.
One thing you can try is to make a new file by using a graphic cut-and-paste from the old file to a new file, using a text editor on the Linux system. In principle, this should not copy any non-printing characters which may be causing trouble.
Rick Venable computational chemist
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OK, I fixed that error, but I still have results 0. Here is a sample of the output:
NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec FSHIft VATOm VFSWIt BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 CGONNB = 0.000 CGOFNB = 10.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions. with mode 5 found 106586 exclusions and 97544 interactions(1-4) found 24112 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 10550403 ATOM PAIRS AND 0 GROUP PAIRS == PRIMARY == SPACE FOR 15825624 ATOM PAIRS AND 0 GROUP PAIRS
General atom nonbond list generation found: 15104476 ATOM PAIRS WERE FOUND FOR ATOM LIST 823754 GROUP PAIRS REQUIRED ATOM SEARCHES
CORREL> enter sr zero CORREL> if ub eq 0 enter ss dupl sr Comparing "0" and "0". IF test evaluated as true. Performing command CORREL> enter sx dupl sr CORREL> if ug eq 0 enter sy dupl sr Comparing "0" and "0". IF test evaluated as true. Performing command CORREL> CORREL> set k 1 Parameter: K <- "1" CORREL> label elp CORREL> if ub eq 0 then Comparing "0" and "0". IF test evaluated as true. Performing command CORREL> enter w@K vect z A @K H@{C}R A @K C2@C Parameter: K -> "1" Parameter: K -> "1" Parameter: C -> "2" Parameter: K -> "1" Parameter: C -> "2" CORREL> enter a@K vect r A @K H@{C}R A @K C2@C Parameter: K -> "1" Parameter: K -> "1" Parameter: C -> "2" Parameter: K -> "1" Parameter: C -> "2" CORREL> enter x@K vect z A @K H@{C}S A @K C2@C Parameter: K -> "1" Parameter: K -> "1" Parameter: C -> "2" Parameter: K -> "1" Parameter: C -> "2" CORREL> enter b@K vect r A @K H@{C}S A @K C2@C Parameter: K -> "1" Parameter: K -> "1" Parameter: C -> "2" Parameter: K -> "1" Parameter: C -> "2" CORREL> else Skip commands until next ENDIF CORREL> if c gt 15 goto eskip
CORREL> ! LOOP OVER LIPIDS; NORM, CALC SCD, ACCUM CORREL> set k 1 Parameter: K <- "1" CORREL> label clp CORREL> mantim w@K ratio a@K ! DIVIDE VECTOR Z BY R (z OF UNIT VECTOR) Parameter: K -> "1" Parameter: K -> "1" NSER: 1 NAMES: W1 TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: VECT VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 3 VALUE: 0.000000 CORREL> mantim w@K squa ! z**2 Parameter: K -> "1" NSER: 1 NAMES: W1 TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: VECT VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 3 VALUE: 0.000000 CORREL> mantim w@K mult 1.5 ! * 3/2 Parameter: K -> "1" NSER: 1 NAMES: W1 TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: VECT VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 3 VALUE: 0.000000 CORREL> mantim w@K shift -0.5 ! - 1/2 Parameter: K -> "1" NSER: 1 NAMES: W1 TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: VECT VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 3 VALUE: 0.000000 CORREL> mantim sr add w@K Parameter: K -> "1" NSER: 1 NAMES: SR TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: ZERO VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 1 VALUE: 0.000000 CORREL> if ub eq 0 then Comparing "0" and "0". IF test evaluated as true. Performing command CORREL> mantim x@K ratio b@K Parameter: K -> "1" Parameter: K -> "1" NSER: 1 NAMES: X1 TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: VECT VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 3 VALUE: 0.000000 CORREL> mantim x@K squa Parameter: K -> "1" NSER: 1 NAMES: X1 TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: VECT VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 3 VALUE: 0.000000 CORREL> mantim x@K mult 1.5 Parameter: K -> "1" NSER: 1 NAMES: X1 TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: VECT VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 3 VALUE: 0.000000 CORREL> mantim x@K shift -0.5 Parameter: K -> "1" NSER: 1 NAMES: X1 TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: VECT VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 3 VALUE: 0.000000 CORREL> mantim ss add x@K Parameter: K -> "1" NSER: 1 NAMES: SS TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: ZERO VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 1 VALUE: 0.000000 CORREL> endif CORREL> if c gt 15 goto mskip Comparing "2" and "15". IF test evaluated as false. Skipping command CORREL> mantim y@K ratio c@K Parameter: K -> "1" Parameter: K -> "1" NSER: 1 NAMES: Y1 TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: VECT VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 3 VALUE: 0.000000 CORREL> mantim y@K squa Parameter: K -> "1" NSER: 1 NAMES: Y1 TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: VECT VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 3 VALUE: 0.000000 CORREL> mantim y@K mult 1.5 Parameter: K -> "1" NSER: 1 NAMES: Y1 TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: VECT VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 3 VALUE: 0.000000 CORREL> mantim y@K shift -0.5 Parameter: K -> "1" NSER: 1 NAMES: Y1 TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: VECT VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 3 VALUE: 0.000000 CORREL> mantim sx add y@K Parameter: K -> "1" NSER: 1 NAMES: SX TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: ZERO VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 1 VALUE: 0.000000 CORREL> if ug eq 0 then Comparing "0" and "0". IF test evaluated as true. Performing command CORREL> mantim z@K ratio d@K Parameter: K -> "1" Parameter: K -> "1" NSER: 1 NAMES: Z1 TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: VECT VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 3 VALUE: 0.000000 CORREL> mantim z@K squa Parameter: K -> "1" NSER: 1 NAMES: Z1 TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: VECT VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 3 VALUE: 0.000000 CORREL> mantim z@K mult 1.5 Parameter: K -> "1" NSER: 1 NAMES: Z1 TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: VECT VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 3 VALUE: 0.000000 CORREL> mantim z@K shift -0.5 Parameter: K -> "1" NSER: 1 NAMES: Z1 TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: VECT VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 3 VALUE: 0.000000 CORREL> mantim sy add z@K Parameter: K -> "1" NSER: 1 NAMES: SY TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: ZERO VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 1 VALUE: 0.000000 CORREL> endif CORREL> label mskip CORREL> incr k by 1 Parameter: K <- "2" CORREL> if k le @NL goto clp Parameter: NL -> "274" Comparing "2" and "274". IF test evaluated as true. Performing command
CORREL> ! use final mantime to set AVER, FLUC for output CORREL> open write unit 1 card name cd@{C}.txt Parameter: C -> "2" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::cd2.txt:: OPNLGU> Unit 1 opened for WRITE access to cd2.txt CORREL> echu 1 CORREL> mantim sr divi @NL Parameter: NL -> "274" NSER: 1 NAMES: SR TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: ZERO VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 1 VALUE: 0.000000 CORREL> echo sr@C ?AVER ?FLUC Parameter: C -> "2" RDCMND substituted energy or value "?AVER" to "0" RDCMND substituted energy or value "?FLUC" to "0" CORREL> if ub eq 0 then Comparing "0" and "0". IF test evaluated as true. Performing command CORREL> mantim ss divi @NL Parameter: NL -> "274" NSER: 1 NAMES: SS TOTALS: 0 AVERAGE: 0.000000 FLUCT: 0.000000 VECCOD: 1 CLASS: ZERO VELCOD: 0 SKIP: 1 DELTA: 0.000000 OFFST: 0.000000 GECOD: 1 VALUE: 0.000000 CORREL> echo ss@C ?AVER ?FLUC Parameter: C -> "2" RDCMND substituted energy or value "?AVER" to "0" RDCMND substituted energy or value "?FLUC" to "0" CORREL> endif CORREL> if c gt 15 goto oskip
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Why do I keep getting 0 results?
SR2 0 0 SS2 0 0 SX2 0 0 SY2 0 0
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Please review the READ BEFORE POSTING guidelines for suggestions on the best way to post output logs.
It looks like you may have omitted the all-important TRAJ command, which actually reads the trajectory file(s) and fills the requested time series with data. The comments in the sample inputs are usually important, such as this one:
! OPEN FILES, FILL SERIES VIA TRAJ
Rick Venable computational chemist
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I didn't ommit. In the script I listed above I included TRAJ command as:
! OPEN FILES, FILL SERIES VIA TRAJ open read unit 1 file name popclipidsnowater.dcd
I have one file only, popclipidsnowater.dcd. What else should I include?
Also, in the output, I got no errors in opening the trajectory file: CORREL> ! OPEN FILES, FILL SERIES VIA TRAJ CORREL> open read unit 1 file name popclipidsnowater.dcd OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::popclipidsnowater.dcd:: OPNLGU> Unit 1 opened for READONLY access to popclipidsnowater.dcd
CORREL>
Thank you,
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