CHARMM Development Project
Dear all,

At the moment,I am trying to run the minimization step of the QM/MM and my scripts is attached.
During the run it was terminated giving the following

rogram received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7f3079aa5d3a
#1 0x7f3079aa4ed5
#2 0x7f307976f20f
#3 0x55aabc3e34d7
#4 0x55aabc3cee34
#5 0x55aabc3cd897
#6 0x55aabc3cedfa
#7 0x55aabc3af6cc
#8 0x55aabc1ad65e
#9 0x55aabba36fc5
#10 0x55aabb91664b
#11 0x55aabb94d675
#12 0x55aabb94e5b2
#13 0x55aabb756d52
#14 0x55aabb753b2e
#15 0x7f30797500b2
#16 0x55aabb753b9d
#17 0xffffffffffffffff
Segmentation fault (core dumped)

I am using C44B1 version of charmm.Can anyone help me to get rid of this?

Thanks
VH

Attached File
step2_minimize.txt  (44 downloads)
I am using QM interface on charmm c44b1 and here is the output file.

CHARMM> open read unit 18 card name "step1_sys_tcts_with_link_atoms.psf" !changing psf to cmp1
VOPEN> Attempting to open::step1_sys_tcts_with_link_atoms.psf::
OPNLGU> Unit 18 opened for READONLY access to step1_sys_tcts_with_link_atoms.psf

CHARMM> read psf unit 18 card
MAINIO> Protein structure file being read from unit 18.
PSFRD2> Reading PSF in the expanded format.
TITLE> * ADD LINK ATOMS
TITLE> * DATE: 1/25/21 10:25:14 CREATED BY USER: virangi
TITLE> *
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 7 Number of residues = 6619
Number of atoms = 27630 Number of groups = 8924
Number of bonds = 27748 Number of angles = 23660
Number of dihedrals = 25862 Number of impropers = 1602
Number of cross-terms = 608
Number of HB acceptors = 6874 Number of HB donors = 13023
Number of NB exclusions = 0 Total charge = 4.00000

CHARMM>

CHARMM> set RADIUS 40
Parameter: RADIUS <- "40"

CHARMM>

CHARMM> set sys tcts_sccdftb ! system from labbook ??
Parameter: SYS <- "TCTS_SCCDFTB"

CHARMM>

CHARMM> open unit 15 read card name "step1_sys_tcts_with_link_atoms.crd"
VOPEN> Attempting to open::step1_sys_tcts_with_link_atoms.crd::
OPNLGU> Unit 15 opened for READONLY access to step1_sys_tcts_with_link_atoms.crd

CHARMM> read coor card unit 15
SPATIAL COORDINATES BEING READ FROM UNIT 15
TITLE> * ADD LINK ATOMS
TITLE> * DATE: 1/25/21 10:25:14 CREATED BY USER: VIRANGI
TITLE> *

CHARMM> close unit 15
VCLOSE: Closing unit 15 with status "KEEP"

CHARMM>

CHARMM> define QM sele (segid R1 .or. segid A1 .or. segid B1 .or. segid C1) show end !
The following atoms are currently set:
SEGId RESId RESName .. TYPEs ..
R1 122 TYR CB HB1 HB2 QQH1 CG CD1 HD1 CE1 HE1 CZ OH HH CD2 HD2 CE2 HE2
A1 611 RET C3 C2 HC1 C1 C12 HC C13 C16 1HC2 2HC2 0HC2 C15 4HC2 5HC2 3HC2 C14 C17 HC8 HC9 1HC1 0HC1 C18 C19 3HC1
2HC1 C20 4HC1 6HC1 5HC1 C5 C6 HC2 HC3 C7 C8 HC4 C9 7HC1 8HC1 9HC1 C10 C11 HC5 HC6 HC7 O H C4 6HC2 7HC2 8HC2
B1 0 FAD C1' N10 HC6 HC5 QQH1 C9A C9 HC7 C8 C7 C7M HC21 HC20 HC22 C6 C5X HC8 N5 C4X H1 C10 N1 H3 C2 N3 O2
H2 C4 O4 C8M HC18 HC19 HC17
C1 25419 TIP3 OH2 H1 H2
SELRPN> 103 atoms have been selected out of 27630

CHARMM> define MM sele .not. QM end
SELRPN> 27527 atoms have been selected out of 27630

CHARMM> !endif
CHARMM>

CHARMM> ! delete atoms sele resname TIP3 end
CHARMM>

CHARMM> !cons fix sele MM end
CHARMM> !mini abnr nstep 100
CHARMM>

CHARMM> open write form unit 13 name check.pdb
VOPEN> Attempting to open::check.pdb::
OPNLGU> Unit 13 opened for WRITE access to check.pdb

CHARMM> write coor pdb unit 13
RDTITL> CLOSE UNIT 13
RDTITL> No title read.
Write CHARMM-pdb format

CHARMM> close unit 13
VCLOSE: Closing unit 13 with status "KEEP"

CHARMM>

CHARMM> scalar WMAIN set 1.0 sele (QM) .and. type P* SHOW end ! main coordinate weights
The following atoms are currently set:
SEGId RESId RESName .. TYPEs ..
SELRPN> 0 atoms have been selected out of 27630

CHARMM> scalar WMAIN set 2.0 sele (QM) .and. type O* SHOW end
The following atoms are currently set:
SEGId RESId RESName .. TYPEs ..
R1 122 TYR OH
A1 611 RET O
B1 0 FAD O2 O4
C1 25419 TIP3 OH2
SELRPN> 5 atoms have been selected out of 27630

CHARMM> scalar WMAIN set 3.0 sele (QM) .and. type N* SHOW end
The following atoms are currently set:
SEGId RESId RESName .. TYPEs ..
B1 0 FAD N10 N5 N1 N3
SELRPN> 4 atoms have been selected out of 27630

CHARMM> scalar WMAIN set 4.0 sele (QM) .and. type C* SHOW end
The following atoms are currently set:
SEGId RESId RESName .. TYPEs ..
R1 122 TYR CB CG CD1 CE1 CZ CD2 CE2
A1 611 RET C3 C2 C1 C12 C13 C16 C15 C14 C17 C18 C19 C20 C5 C6 C7 C8 C9 C10 C11 C4
B1 0 FAD C1' C9A C9 C8 C7 C7M C6 C5X C4X C10 C2 C4 C8M
SELRPN> 40 atoms have been selected out of 27630

CHARMM> scalar WMAIN set 5.0 sele (QM) .and. type H* SHOW end
The following atoms are currently set:
SEGId RESId RESName .. TYPEs ..
R1 122 TYR HB1 HB2 HD1 HE1 HH HD2 HE2
A1 611 RET HC1 HC HC8 HC9 HC2 HC3 HC4 HC5 HC6 HC7 H
B1 0 FAD HC6 HC5 HC7 HC21 HC20 HC22 HC8 H1 H3 H2 HC18 HC19 HC17
C1 25419 TIP3 H1 H2
SELRPN> 33 atoms have been selected out of 27630

CHARMM> scalar WMAIN set 5.0 sele (QM) .and. type QQH1 SHOW end
The following atoms are currently set:
SEGId RESId RESName .. TYPEs ..
R1 122 TYR QQH1
B1 0 FAD QQH1
SELRPN> 2 atoms have been selected out of 27630

CHARMM> !endif
CHARMM> ! Do not forget about the link atom
CHARMM>

CHARMM> update atom fshift noextend cdie vdw vfswitch eps 1.0 - ! constant dielectric and classical force shift method
CHARMM> cutnb 14 ctofnb 12 ctonnb 10.0 -
CHARMM> WMIN 1.5 inbfrq -1

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 45413 exclusions and 25401 interactions(1-4)
found 8590 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 7939526 ATOM PAIRS AND 0 GROUP PAIRS
== PRIMARY == SPACE FOR 11909309 ATOM PAIRS AND 0 GROUP PAIRS
== PRIMARY == SPACE FOR 17863984 ATOM PAIRS AND 0 GROUP PAIRS

General atom nonbond list generation found:
13377773 ATOM PAIRS WERE FOUND FOR ATOM LIST
791533 GROUP PAIRS REQUIRED ATOM SEARCHES


CHARMM>

CHARMM> !WE WILL NOW GO THROUGH A SERIES OF MINIMIZATIONS
CHARMM>

CHARMM> define backbone sele segid RIC .and. (type C .or. type CA .or. type O .or. type N) end
SELRPN> 0 atoms have been selected out of 27630

CHARMM> define include sele .byres. (point 0.0 0.0 0.0 cut @RADIUS) end
Parameter: RADIUS -> "40"
SELRPN> 27265 atoms have been selected out of 27630

CHARMM> define outside sele .not. include end
SELRPN> 365 atoms have been selected out of 27630

CHARMM> !Keep outside fix ALL the time
CHARMM> cons fix sele .not. include end ! Everything outside is fixed
SELRPN> 365 atoms have been selected out of 27630

CHARMM>

CHARMM> shake bonh tol 1.0e-10 param sele .not. QM end
SELRPN> 27527 atoms have been selected out of 27630
SHKCOM> SHAKE parameters: TOL = 0.1000D-09 MXITer = 500

22617 constraints will held by SHAKE.

CHARMM>

CHARMM> !NOW WE WILL WORK WITH INCLUDE
CHARMM>

CHARMM> sccdftb remove SELE QM end - ! classical energies within QM atoms are removed
CHARMM> TEMP 0.00 SCFT 0.000001 EXGR - ! electronic temp (fermi) , convergence criteria
CHARMM> chrg 0.012 HBON D3RD mull ! MIXE 1 !slash NOC RC 50 BA 2 LT 5 !without dispersion
SELRPN> 103 atoms have been selected out of 27630
SCCINT> REMOve: Classical energies within QM atoms are removed.
SCCINT> EXGRoup: QM/MM Electrostatics for link host groups removed.
SCCINT> No QINP: Charges will be based on atomic numbers.
WARNING FROM DECODI - REAL to INTEGER conversion
0.012
Integer portion will be returned.
SCCINT> Running SCC-DFTB via EGLCAO code.
SCCINT> LAPACK DSYGV* requested as diagonalizer, but DFTBMKL is not present.
SCCINT> Use EWEVGE as diagonalizer
SCCINT> DO NOT USE CUT-OFF FOR QM/MM
Mulliken population requested
Use Hbond Correction
Use Full Third Order SCC
------------------------------------------------
SCCINT: Classical atoms excluded from the QM calculation:
1859 PROA 122 TYR N
1860 PROA 122 TYR HN
1861 PROA 122 TYR CA
1862 PROA 122 TYR HA
9510 HETB 0 FAD C2'
9511 HETB 0 FAD O2'
9512 HETB 0 FAD HC4
9513 HETB 0 FAD H4
SCCINT: Quantum mechanical atoms:
27528 R1 122 TYR CB
27529 R1 122 TYR HB1
27530 R1 122 TYR HB2
27532 R1 122 TYR CG
27533 R1 122 TYR CD1
27534 R1 122 TYR HD1
27535 R1 122 TYR CE1
27536 R1 122 TYR HE1
27537 R1 122 TYR CZ
27538 R1 122 TYR OH
27539 R1 122 TYR HH
27540 R1 122 TYR CD2
27541 R1 122 TYR HD2
27542 R1 122 TYR CE2
27543 R1 122 TYR HE2
27544 A1 611 RET C3
27545 A1 611 RET C2
27546 A1 611 RET HC1
27547 A1 611 RET C1
27548 A1 611 RET C12
27549 A1 611 RET HC
27550 A1 611 RET C13
27551 A1 611 RET C16
27552 A1 611 RET 1HC2
27553 A1 611 RET 2HC2
27554 A1 611 RET 0HC2
27555 A1 611 RET C15
27556 A1 611 RET 4HC2
27557 A1 611 RET 5HC2
27558 A1 611 RET 3HC2
27559 A1 611 RET C14
27560 A1 611 RET C17
27561 A1 611 RET HC8
27562 A1 611 RET HC9
27563 A1 611 RET 1HC1
27564 A1 611 RET 0HC1
27565 A1 611 RET C18
27566 A1 611 RET C19
27567 A1 611 RET 3HC1
27568 A1 611 RET 2HC1
27569 A1 611 RET C20
27570 A1 611 RET 4HC1
27571 A1 611 RET 6HC1
27572 A1 611 RET 5HC1
27573 A1 611 RET C5
27574 A1 611 RET C6
27575 A1 611 RET HC2
27576 A1 611 RET HC3
27577 A1 611 RET C7
27578 A1 611 RET C8
27579 A1 611 RET HC4
27580 A1 611 RET C9
27581 A1 611 RET 7HC1
27582 A1 611 RET 8HC1
27583 A1 611 RET 9HC1
27584 A1 611 RET C10
27585 A1 611 RET C11
27586 A1 611 RET HC5
27587 A1 611 RET HC6
27588 A1 611 RET HC7
27589 A1 611 RET O
27590 A1 611 RET H
27591 A1 611 RET C4
27592 A1 611 RET 6HC2
27593 A1 611 RET 7HC2
27594 A1 611 RET 8HC2
27595 B1 0 FAD C1'
27596 B1 0 FAD N10
27597 B1 0 FAD HC6
27598 B1 0 FAD HC5
27600 B1 0 FAD C9A
27601 B1 0 FAD C9
27602 B1 0 FAD HC7
27603 B1 0 FAD C8
27604 B1 0 FAD C7
27605 B1 0 FAD C7M
27606 B1 0 FAD HC21
27607 B1 0 FAD HC20
27608 B1 0 FAD HC22
27609 B1 0 FAD C6
27610 B1 0 FAD C5X
27611 B1 0 FAD HC8
27612 B1 0 FAD N5
27613 B1 0 FAD C4X
27614 B1 0 FAD H1
27615 B1 0 FAD C10
27616 B1 0 FAD N1
27617 B1 0 FAD H3
27618 B1 0 FAD C2
27619 B1 0 FAD N3
27620 B1 0 FAD O2
27621 B1 0 FAD H2
27622 B1 0 FAD C4
27623 B1 0 FAD O4
27624 B1 0 FAD C8M
27625 B1 0 FAD HC18
27626 B1 0 FAD HC19
27627 B1 0 FAD HC17
27628 C1 25419 TIP3 OH2
27629 C1 25419 TIP3 H1
27630 C1 25419 TIP3 H2
SCCINT: Quantum mechanical link atoms:
27531 R1 122 TYR QQH1
27599 B1 0 FAD QQH1
SCCINT: Quantum mechanical GHO boundary atoms:
NONE.
------------------------------------------------
FINDEL: Quantum atom 27528 R1 122 TYR CB assigned to element: C 6
FINDEL: Quantum atom 27529 R1 122 TYR HB1 assigned to element: H 1
FINDEL: Quantum atom 27530 R1 122 TYR HB2 assigned to element: H 1
FINDEL: Quantum atom 27531 R1 122 TYR QQH1 assigned to element: QQH1 1
FINDEL: Quantum atom 27532 R1 122 TYR CG assigned to element: C 6
FINDEL: Quantum atom 27533 R1 122 TYR CD1 assigned to element: C 6
FINDEL: Quantum atom 27534 R1 122 TYR HD1 assigned to element: H 1
FINDEL: Quantum atom 27535 R1 122 TYR CE1 assigned to element: C 6
FINDEL: Quantum atom 27536 R1 122 TYR HE1 assigned to element: H 1
FINDEL: Quantum atom 27537 R1 122 TYR CZ assigned to element: C 6
FINDEL: Quantum atom 27538 R1 122 TYR OH assigned to element: O 8
FINDEL: Quantum atom 27539 R1 122 TYR HH assigned to element: H 1
FINDEL: Quantum atom 27540 R1 122 TYR CD2 assigned to element: C 6
FINDEL: Quantum atom 27541 R1 122 TYR HD2 assigned to element: H 1
FINDEL: Quantum atom 27542 R1 122 TYR CE2 assigned to element: C 6
FINDEL: Quantum atom 27543 R1 122 TYR HE2 assigned to element: H 1
FINDEL: Quantum atom 27544 A1 611 RET C3 assigned to element: C 6
FINDEL: Quantum atom 27545 A1 611 RET C2 assigned to element: C 6
FINDEL: Quantum atom 27546 A1 611 RET HC1 assigned to element: H 1
FINDEL: Quantum atom 27547 A1 611 RET C1 assigned to element: C 6
FINDEL: Quantum atom 27548 A1 611 RET C12 assigned to element: C 6
FINDEL: Quantum atom 27549 A1 611 RET HC assigned to element: H 1
FINDEL: Quantum atom 27550 A1 611 RET C13 assigned to element: C 6
FINDEL: Quantum atom 27551 A1 611 RET C16 assigned to element: C 6
FINDEL: Quantum atom 27552 A1 611 RET 1HC2 assigned to element: H 1
FINDEL: Quantum atom 27553 A1 611 RET 2HC2 assigned to element: H 1
FINDEL: Quantum atom 27554 A1 611 RET 0HC2 assigned to element: H 1
FINDEL: Quantum atom 27555 A1 611 RET C15 assigned to element: C 6
FINDEL: Quantum atom 27556 A1 611 RET 4HC2 assigned to element: H 1
FINDEL: Quantum atom 27557 A1 611 RET 5HC2 assigned to element: H 1
FINDEL: Quantum atom 27558 A1 611 RET 3HC2 assigned to element: H 1
FINDEL: Quantum atom 27559 A1 611 RET C14 assigned to element: C 6
FINDEL: Quantum atom 27560 A1 611 RET C17 assigned to element: C 6
FINDEL: Quantum atom 27561 A1 611 RET HC8 assigned to element: H 1
FINDEL: Quantum atom 27562 A1 611 RET HC9 assigned to element: H 1
FINDEL: Quantum atom 27563 A1 611 RET 1HC1 assigned to element: H 1
FINDEL: Quantum atom 27564 A1 611 RET 0HC1 assigned to element: H 1
FINDEL: Quantum atom 27565 A1 611 RET C18 assigned to element: C 6
FINDEL: Quantum atom 27566 A1 611 RET C19 assigned to element: C 6
FINDEL: Quantum atom 27567 A1 611 RET 3HC1 assigned to element: H 1
FINDEL: Quantum atom 27568 A1 611 RET 2HC1 assigned to element: H 1
FINDEL: Quantum atom 27569 A1 611 RET C20 assigned to element: C 6
FINDEL: Quantum atom 27570 A1 611 RET 4HC1 assigned to element: H 1
FINDEL: Quantum atom 27571 A1 611 RET 6HC1 assigned to element: H 1
FINDEL: Quantum atom 27572 A1 611 RET 5HC1 assigned to element: H 1
FINDEL: Quantum atom 27573 A1 611 RET C5 assigned to element: C 6
FINDEL: Quantum atom 27574 A1 611 RET C6 assigned to element: C 6
FINDEL: Quantum atom 27575 A1 611 RET HC2 assigned to element: H 1
FINDEL: Quantum atom 27576 A1 611 RET HC3 assigned to element: H 1
FINDEL: Quantum atom 27577 A1 611 RET C7 assigned to element: C 6
FINDEL: Quantum atom 27578 A1 611 RET C8 assigned to element: C 6
FINDEL: Quantum atom 27579 A1 611 RET HC4 assigned to element: H 1
FINDEL: Quantum atom 27580 A1 611 RET C9 assigned to element: C 6
FINDEL: Quantum atom 27581 A1 611 RET 7HC1 assigned to element: H 1
FINDEL: Quantum atom 27582 A1 611 RET 8HC1 assigned to element: H 1
FINDEL: Quantum atom 27583 A1 611 RET 9HC1 assigned to element: H 1
FINDEL: Quantum atom 27584 A1 611 RET C10 assigned to element: C 6
FINDEL: Quantum atom 27585 A1 611 RET C11 assigned to element: C 6
FINDEL: Quantum atom 27586 A1 611 RET HC5 assigned to element: H 1
FINDEL: Quantum atom 27587 A1 611 RET HC6 assigned to element: H 1
FINDEL: Quantum atom 27588 A1 611 RET HC7 assigned to element: H 1
FINDEL: Quantum atom 27589 A1 611 RET O assigned to element: O 8
FINDEL: Quantum atom 27590 A1 611 RET H assigned to element: H 1
FINDEL: Quantum atom 27591 A1 611 RET C4 assigned to element: C 6
FINDEL: Quantum atom 27592 A1 611 RET 6HC2 assigned to element: H 1
FINDEL: Quantum atom 27593 A1 611 RET 7HC2 assigned to element: H 1
FINDEL: Quantum atom 27594 A1 611 RET 8HC2 assigned to element: H 1
FINDEL: Quantum atom 27595 B1 0 FAD C1' assigned to element: C 6
FINDEL: Quantum atom 27596 B1 0 FAD N10 assigned to element: N 7
FINDEL: Quantum atom 27597 B1 0 FAD HC6 assigned to element: H 1
FINDEL: Quantum atom 27598 B1 0 FAD HC5 assigned to element: H 1
FINDEL: Quantum atom 27599 B1 0 FAD QQH1 assigned to element: QQH1 1
FINDEL: Quantum atom 27600 B1 0 FAD C9A assigned to element: C 6
FINDEL: Quantum atom 27601 B1 0 FAD C9 assigned to element: C 6
FINDEL: Quantum atom 27602 B1 0 FAD HC7 assigned to element: H 1
FINDEL: Quantum atom 27603 B1 0 FAD C8 assigned to element: C 6
FINDEL: Quantum atom 27604 B1 0 FAD C7 assigned to element: C 6
FINDEL: Quantum atom 27605 B1 0 FAD C7M assigned to element: C 6
FINDEL: Quantum atom 27606 B1 0 FAD HC21 assigned to element: H 1
FINDEL: Quantum atom 27607 B1 0 FAD HC20 assigned to element: H 1
FINDEL: Quantum atom 27608 B1 0 FAD HC22 assigned to element: H 1
FINDEL: Quantum atom 27609 B1 0 FAD C6 assigned to element: C 6
FINDEL: Quantum atom 27610 B1 0 FAD C5X assigned to element: C 6
FINDEL: Quantum atom 27611 B1 0 FAD HC8 assigned to element: H 1
FINDEL: Quantum atom 27612 B1 0 FAD N5 assigned to element: N 7
FINDEL: Quantum atom 27613 B1 0 FAD C4X assigned to element: C 6
FINDEL: Quantum atom 27614 B1 0 FAD H1 assigned to element: H 1
FINDEL: Quantum atom 27615 B1 0 FAD C10 assigned to element: C 6
FINDEL: Quantum atom 27616 B1 0 FAD N1 assigned to element: N 7
FINDEL: Quantum atom 27617 B1 0 FAD H3 assigned to element: H 1
FINDEL: Quantum atom 27618 B1 0 FAD C2 assigned to element: C 6
FINDEL: Quantum atom 27619 B1 0 FAD N3 assigned to element: N 7
FINDEL: Quantum atom 27620 B1 0 FAD O2 assigned to element: O 8
FINDEL: Quantum atom 27621 B1 0 FAD H2 assigned to element: H 1
FINDEL: Quantum atom 27622 B1 0 FAD C4 assigned to element: C 6
FINDEL: Quantum atom 27623 B1 0 FAD O4 assigned to element: O 8
FINDEL: Quantum atom 27624 B1 0 FAD C8M assigned to element: C 6
FINDEL: Quantum atom 27625 B1 0 FAD HC18 assigned to element: H 1
FINDEL: Quantum atom 27626 B1 0 FAD HC19 assigned to element: H 1
FINDEL: Quantum atom 27627 B1 0 FAD HC17 assigned to element: H 1
FINDEL: Quantum atom 27628 C1 25419 TIP3 OH2 assigned to element: O 8
FINDEL: Quantum atom 27629 C1 25419 TIP3 H1 assigned to element: H 1
FINDEL: Quantum atom 27630 C1 25419 TIP3 H2 assigned to element: H 1

SCCDFN> Some atoms will be treated quantum mechanically.

The number of SCCDFTB QM atoms = 103
The number of molecular mechanical atoms = 27527
The number of MM atoms excluded from QM = 8
Of which the number of QM/MM link atoms = 2


CHARGE OF SCCDFTB ATOMS: 0
** dftb **
enter mode, fmax, scf, scftol, read charge,dispers,EXT
Number of QM atoms in dylcao: 103
skip struc. file,atoms from charmm: 103 27519
enter filename for output structure
DYLCAO> Mixer used is: Broyden mixer
skfile for pair 1 1 :./mio-1-1/P-P.skf
skfile for pair 1 2 :mio-1-1/P-O.skf
skfile for pair 1 3 :mio-1-1/P-N.skf
skfile for pair 1 4 :mio-1-1/P-C.skf
skfile for pair 1 5 :mio-1-1/P-H.skf
skfile for pair 2 1 :mio-1-1/O-P.skf
skfile for pair 2 2 :mio-1-1/O-O.skf
skfile for pair 2 3 :mio-1-1/O-N.skf
skfile for pair 2 4 :mio-1-1/O-C.skf
skfile for pair 2 5 :mio-1-1/O-H.skf
skfile for pair 3 1 :mio-1-1/N-P.skf
skfile for pair 3 2 :mio-1-1/N-O.skf
skfile for pair 3 3 :mio-1-1/N-N.skf
skfile for pair 3 4 :mio-1-1/N-C.skf
skfile for pair 3 5 :mio-1-1/N-H.skf
skfile for pair 4 1 :mio-1-1/C-P.skf
skfile for pair 4 2 :mio-1-1/C-O.skf
skfile for pair 4 3 :mio-1-1/C-N.skf
skfile for pair 4 4 :mio-1-1/C-C.skf
skfile for pair 4 5 :mio-1-1/C-H.skf
skfile for pair 5 1 :mio-1-1/H-P.skf
skfile for pair 5 2 :mio-1-1/H-O.skf
skfile for pair 5 3 :mio-1-1/H-N.skf
skfile for pair 5 4 :mio-1-1/H-C.skf
skfile for pair 5 5 :mio-1-1/H-H.skf
Total charge of SCCDFTB molecule: 0
Total number of electrons: 245.00000000000000
Reading in derivative of Hubbard para
Hubbard derivative: 1 P -0.14000000000000001
Hubbard derivative: 2 O -0.19000000000000000
Hubbard derivative: 3 N -0.13000000000000000
Hubbard derivative: 4 C -0.23000000000000001
Hubbard derivative: 5 H -0.16000000000000000
Reading in hbond correction parameter: kl1
Hbond correction parameter: kl1: 4.2000000000000002
Hbond is invoked for atom pairs where at least oneatom is of nuclear charge equals one

CHARMM>

CHARMM> !#######################################################
CHARMM>

CHARMM> !#################################################
CHARMM> energy

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 13377773 atom pairs and 70814 atom exclusions.
There are 0 group pairs and 8590 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 17863984 ATOM PAIRS AND 0 GROUP PAIRS

General atom nonbond list generation found:
13357491 ATOM PAIRS WERE FOUND FOR ATOM LIST
791303 GROUP PAIRS REQUIRED ATOM SEARCHES




This run stop at the minimization without giving an error. I really don't understand what's going in here

can someone help me on this?

Thanks
VH
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