VMD-L Mailing List
From: Jerry Xu (jerryx_at_hotmail.com)
Date: Thu Jul 15 2004 - 13:03:30 CDT
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Thanks so much for everybody's useful suggestion, and sorry for unclear
error message that I provided, here is the detail error message . ( I didnot
really count atom number or residue number, I just use same method to check
some smaller protein then it works, but when I check little larger protein,
charmm will just give me such error message) .
CHARMM> open unit 1 read form name @pdbfile.psf
Parameter: PDBFILE -> "/HOME/JERRY/1A30-A"
VOPEN> Attempting to open::/home/jerry/1a30-a.psf::
OPNLGU> Unit 1 opened for READONLY access to /home/jerry/1a30-a.psf
CHARMM> read psf card unit 1
MAINIO> Protein structure file being read from unit 1.
TITLE> REMARKS original generated structure charmm psf file
TITLE> *
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 1 Number of residues =
99
Number of atoms = 1569 Number of groups =
1
Number of bonds = 1582 Number of angles =
2898
Number of dihedrals = 4233 Number of impropers =
247
Number of HB acceptors = 0 Number of HB donors =
0
Number of NB exclusions = 0 Total charge = 3.00000
CHARMM> close unit 1
VCLOSE: Closing unit 1 with status "KEEP"
CHARMM>
CHARMM> open unit 1 read form name @pdbfile.pdb
Parameter: PDBFILE -> "/HOME/JERRY/1A30-A"
VOPEN> Attempting to open::/home/jerry/1a30-a.pdb::
OPNLGU> Unit 1 opened for READONLY access to /home/jerry/1a30-a.pdb
CHARMM> read coor pdb unit 1
SPATIAL COORDINATES BEING READ FROM UNIT 1
TITLE> ORIGINAL GENERATED COORDINATE PDB
FILE/HOME/JERRY/1A30-A/HOME/JERRY/1A30-
TITLE> *
CHARMM> close unit 1
VCLOSE: Closing unit 1 with status "KEEP"
CHARMM> ENERGY
NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch
BYGRoup NOEXtnd NOEWald
CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
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.
<MAKINB> with mode 5 found 4480 exclusions and 4173 interactions(1-4)
***** LEVEL -3 WARNING FROM <MAKGRP> *****
***** maximum number of atoms per group exceeded
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 2
/---------\
/ \
/ \
/ \
! 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
MAXIMUM STACK SPACE USED IS 47526
STACK CURRENTLY IN USE IS 5140
MOST SEVERE WARNING WAS AT LEVEL -3
HEAP PRINTOUT- HEAP SIZE 2048000
SPACE CURRENTLY IN USE IS 22732
MAXIMUM SPACE USED IS 71276
FREE LIST
PRINHP> ADDRESS: 1 LENGTH: 2024796 NEXT: 2047529
PRINHP> ADDRESS: 2047529 LENGTH: 472 NEXT: 0
$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 0.86 SECONDS
CPU TIME: 0.79 SECONDS
/*************************************************************************************/
Sincerely yours
Jerry
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- Next message: Bogdan Costescu: "Re: vmd psfgen problem with CHARMM"
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- Maybe in reply to: John Stone: "Re: vmd psfgen problem with CHARMM"
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- Reply: Bogdan Costescu: "Re: vmd psfgen problem with CHARMM"
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