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

[Maik Goette]

Be aware, that you can't use the ouput with every forcefield...
Attaching the gro-file to your protein gro at the proper position (right 
after the protein) and building the correct topology should do the job.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


mjduan wrote:
> Yes, I found a server (ProDrg) can get the .gro and .top files of ATP
> molecule.
> 
> 
> ---------------------------
> Whereas one should also mention, that ATP isn't included in every
> forcefield, GROMACS supports...
> So probably, parameterization has to be done also.
> 
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
>         mgoette2[at]gwdg.de
> WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
> 
> 
> Mark Abraham wrote:
>> mjduan at smail.hust.edu.cn 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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