VMD-L Mailing List

From: Jerry Xu (jerryx_at_hotmail.com)
Date: Thu Jul 15 2004 - 13:03:30 CDT

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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