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

[TJ Piggot]

Hi,

If you are using any of the united atom GROMOS96 forcefields then there is 
already an rtp entry for ATP. Check out the .rtp files in the top folder. 
All you need to do is to have the ATP atoms in the pdb file the same as the 
atom names in the .rtp file for pdb2gmx to do all the work for you. If you 
are not using a united atom forcefield then you will have to get your 
parameters for ATP from somewhere else (or calculate them yourself - not 
easy).

Hope this helps

Tom

--On Thursday, August 09, 2007 10:03:30 +0200 Maik Goette 
<mgoette at mpi-bpc.mpg.de> wrote:

> 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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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.