Analysis of NAMD output with CHARMM

From: Leyla Celik (lc_at_chem.au.dk)
Date: Mon Feb 14 2005 - 02:47:42 CST

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

-- 
Leyla Celik
Ph.d. student
Department of Chemistry
University of Aarhus
Langelandsgade 140
DK-8000 Aarhus C
Denmark
Tel: +45 8942 3869
e-mail: lc_at_chem.au.dk

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:31 CST