Re: ATP molecule

From: Per Jr. Greisen (greisen_at_binf.ku.dk)
Date: Thu Jul 19 2007 - 13:23:24 CDT

Hi,

hmmmm - I was able to generate the psf using vmd with the topology file -
I have not tested the script but have you tried to generate the psf and
guess coordinates?

writepsf OUT/test_psfgen_1.psf
guesscoord
writepdb OUT/test_psfgen_1.pdb

> 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
>>
>>
>>
>

-- 
Best Regards
Per Jr. Greisen

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