[gmx-users] how to simulate a protein and a ATP molecule simultaneity?

Maik Goette mgoette at mpi-bpc.mpg.de
Thu Aug 9 09:50:26 CEST 2007

As Mark suggested. If you have the parameters for your ATP, build an
RTP-entry and afterwards, give the protein together with ATP into pdb2gmx...

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

mjduan at smail.hust.edu.cn wrote:
> Thank u very much for your suggestion, and now I had get the .gro file 
> and .top file of ATP molecule, but how to I add the ATP molecule into 
> the .gro and .top files of the protein? (If I paste the ATP's datas to 
> the end of protein's file directly, and do genbox, then the result (.gro 
> /.top file) only contain the atoms of the protein and water.)
> And is there any difference between the .mdp file to do grompp for this 
> complex and for the system only contain protein and water?
> mjduan at smail.hust.edu.cn <http://www.gromacs.org/mailman/listinfo/gmx-users> wrote:
>>/ Dear GROMACS users:
> />/ I want to simulate a complex composed by a protein and an ATP molecule, 
> />/ and when I use the pdb2gmx to build the topology file and transfer 
> />/ the*pdb* file to *gro* file,
>   it said "/Fatal error: Atom PG in residue 
> />/ ATP 1 not found in rtp entry with 36 atoms while sorting atoms/", So how 
> />/ can I build the *top* file and *gro* file for ATP molecular and simulate 
> />/ the protein molcular and ATP molecule simultaneity?
> /
> By reading chapter 5 of the manual thoroughly, understanding how the rtp
> files work for your force field and modifying your .pdb file and/or
> force field files to work suitably.
> Mark
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