From: Nathalie Reuter (Nathalie.Reuter_at_bccs.uib.no)
Date: Mon Feb 14 2005 - 07:21:56 CST
Hi,
are you sure it is the psf that causes problems?
Could it be the PDB file? Either that you have too many water molecules
per segment or that Charmm does not read the pdb correctly. I have had
problems reading pdb files with the latest versions of Charmm. How did
you generate the input PDB for your simulation? Psfgen or charmm ?
Nathalie
Leyla Celik wrote:
>Hi,
>
>I am trying to use CHARMM to analyse my NAMD outputs. I have generated a CHARMM
>psf-file with psfgen and "writepsf charmm name.psf", but when I read the psf
>and pdb file in CHARMM i terminates with a warning about atoms per group
>exceeded.
>
>I have posted the relevant part of the output below.
>
>Hope anyone can help me.
>
>Leyla
>
>
>
> CHARMM> OPEN READ UNIT 1 CARD NAME "CPSF/3ert_charmm.psf"
> VOPEN> Attempting to open::CPSF/3ert_charmm.psf::
> OPNLGU> Unit 1 opened for READONLY access to CPSF/3ert_charmm.psf
>
> CHARMM> READ PSF UNIT 1 CARD
> 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 = 11 Number of residues = 12080
> Number of atoms = 39548 Number of groups = 1
> Number of bonds = 39590 Number of angles = 19283
> Number of dihedrals = 10881 Number of impropers = 678
> Number of HB acceptors = 0 Number of HB donors = 0
> Number of NB exclusions = 0 Total charge = 0.00000
>
> CHARMM> CLOSE UNIT 1
> VCLOSE: Closing unit 1 with status "KEEP"
>
> CHARMM> !
> CHARMM> OPEN READ UNIT 1 CARD NAME "../heat_450K.pdb"
> VOPEN> Attempting to open::../heat_450K.pdb::
> OPNLGU> Unit 1 opened for READONLY access to ../heat_450K.pdb
>
> CHARMM> READ COOR PDB UNIT 1
> SPATIAL COORDINATES BEING READ FROM UNIT 1
> TITLE> FINAL COORDINATES WRITTEN BY NAMD AT TIMESTEP 30000
> TITLE> *
>
> ** WARNING ** For atom in coordinate file, could not find residue in PSF, and
>is thus ignored:
>
> SEGID=WT1 RESID=000 RESNAME= TIP3 TYPE= OH2
> *** LEVEL 1 WARNING *** BOMLEV IS -3
>
> ** WARNING ** For atom in coordinate file, could not find residue in PSF, and
>is thus ignored:
>
> SEGID=WT1 RESID=000 RESNAME= TIP3 TYPE= H1
> *** LEVEL 1 WARNING *** BOMLEV IS -3
>
> ** WARNING ** For atom in coordinate file, could not find residue in PSF, and
>is thus ignored:
>
> SEGID=WT1 RESID=000 RESNAME= TIP3 TYPE= H2
> *** LEVEL 1 WARNING *** BOMLEV IS -3
>
> ** WARNING ** For atom in coordinate file, could not find residue in PSF, and
>is thus ignored:
>
> SEGID=WT1 RESID=001 RESNAME= TIP3 TYPE= OH2
> *** LEVEL 1 WARNING *** BOMLEV IS -3
> ** WARNING ** After reading, there are no coordinates for selected atom: 7095
>1263 TIP3 OH2
> ** WARNING ** After reading, there are no coordinates for selected atom: 7096
>1263 TIP3 H1
> ** WARNING ** After reading, there are no coordinates for selected atom: 7097
>1263 TIP3 H2
> ** WARNING ** After reading, there are no coordinates for selected atom: 7098
>1264 TIP3 OH2
> ** WARNING ** After reading, there are no coordinates for selected atom: 7099
>1264 TIP3 H1
> ** WARNING ** After reading, there are no coordinates for selected atom: 7100
>1264 TIP3 H2
> ** WARNING ** After reading, there are no coordinates for selected atom: 7101
>1265 TIP3 OH2
> ** WARNING ** After reading, there are no coordinates for selected atom: 7102
>1265 TIP3 H1
> ** WARNING ** After reading, there are no coordinates for selected atom: 7103
>1265 TIP3 H2
> ** WARNING ** After reading, there are no coordinates for selected atom: 7104
>1266 TIP3 OH2
>
> ** A total of 30111 selected atoms have no coordinates
>
> ** WARNING ** Coordinates were overwritten for 17358 atoms.
>
> ** MESSAGE ** 12753 atoms in coordinate file were outside the specified
>sequence range.
> *** LEVEL 2 WARNING *** BOMLEV IS -3
>
> CHARMM> CLOSE UNIT 1
> VCLOSE: Closing unit 1 with status "KEEP"
>
> CHARMM> !
> CHARMM> !
> CHARMM> CORREL MAXTIME 2000000 MAXSERIES 50 MAXATOMS 100
>
> **** WARNING: SOFT CORE POTENTIAL IS AVAILABLE ONLY WITH :
> VSWIT, VFSHIFT, CFSWIT, CSWIT, RSHIFT, RSWIT
>
> 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 47041 exclusions and 10697 interactions(1-4)
>
> ***** LEVEL -3 WARNING FROM <MAKGRP> *****
> ***** maximum number of atoms per group exceeded
> ******************************************
> BOMLEV ( -3) IS REACHED - TERMINATING. WRNLEV IS 5
>
>
>
>
>
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