Re: Analysis of NAMD output with CHARMM

From: Leyla Celik (lc_at_chem.au.dk)
Date: Mon Feb 14 2005 - 07:48:28 CST

Hi,

I have tried with both pdb from psfgen and a pdb file from my NAMD simulation,
none works. One of the problems might be, that there is a column shift when
going from residue 999 to 1000, where Charmm keeps resid's to the left, while
NAMD keeps them to the right.

I have not been able to generate a reasonable pdb file with charmm due to the
same resid's.

/Leyla

Citat Nathalie Reuter <Nathalie.Reuter_at_bccs.uib.no>:

> 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
> >
> >
> >
> >
> >
>
>

-- 
Leyla Celik
Kemisk Institut
Aarhus Universitet
Langelandsgade 140
8000 Århus C
Danmark
Tlf: +45 8942 3869
e-mail: lc_at_chem.au.dk

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