Re: ATP molecule

From: snoze pa (snoze.pa_at_gmail.com)
Date: Thu Jul 19 2007 - 12:40:35 CDT

Michel,
sine ATP molecule is insiide toppar_all27_na_nad_ppi.str file. so I am using
this script.
mkdir OUT
grep 'ATP' input.pdb > OUT/test_ATP.pdb
/usr/local/NAMD/psfgen << ENDMOL
########################################
topology top_all27_prot_lipid_ori.inp
topology toppar_all27_na_nad_ppi.str
########################################
########################################
segment 1B4H {
 pdb OUT/test_ATP.pdb
  }
coordpdb OUT/test_ATP.pdb 1B4H
###### guesscoord
########################################
guesscoord
writepsf OUT/test_psfgen_1.psf
writepdb OUT/test_psfgen_1.pdb
ENDMOL

ATP molecule is also atttached. but I am getting following error message

*************************************************************
*** Demonstration of psfgen - NAMD psf file generator ***
*************************************************************

*** creating OUT directory ***
*** splitting OUT PDB file into segments ***
PSFGEN from NAMD 2.6 for Linux-i686
reading topology file top_all27_prot_lipid_ori.inp

>>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
from
>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
and
  \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
  \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
              Alexander D. MacKerell Jr.
                     August 1999
 All comments to ADM jr. email: alex,mmiris.ab.umd.edu
              telephone: 410-706-7442

Created by CHARMM version 27 1
reading topology file toppar_all27_na_nad_ppi.str

 CHARMM27 All-Hydrogen Nucleic Acid Force Toppar Stream File
 NAD+, NADH, ADP, ATP, PPI and related analogs
 A.D. MacKerell, Jr., July 2001
 stream following RTF and PARAM read of

reading topology from stream file
 NAD, PPI topology

Created by CHARMM version 31 1
skipping statements at end of file due to end or return statement
building segment 1B4H
reading residues from pdb file OUT/test_ATP.pdb
extracted 2 residues from pdb file
Info: generating structure...
unknown atom type ON3
add atom failed in residue ATP:2001
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

On 7/19/07, Per Jr. Greisen <greisen_at_binf.ku.dk> wrote:
>
> which error does it give u?
>
>
>
>
> > Dear NAMD Users,
> > I want to simulate ATP molecule, which is in toppar_all27...str file.
> > Somehow, psfgen is not accepting the charmm str file.
> > Anybody can help me how can I use .str parameter file in psfgen.
> > thanks in advance.
> >
>
>
> --
> Best Regards
>
> Per Jr. Greisen
>
>
>


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