[gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.

[Maik Goette]

Chris

This is, what I usually do, too.
Still you need the parameters for your ligand from somewhere ;)

Regards

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/


Chris Neale wrote:
> When actually building the topology I find it easiest to create the 
> residues in the relevant .rtp and allow pdb2gmx to build the topology 
> for you. However, all this does is correctly connect everything and put 
> your parameters where they should be. All previous comments (in this 
> thread and the hundreds of other threads on this topic) still apply 
> about how to come up with the parameters... read the original papers and 
> reproduce their methodology.
> 
> Chris.
> 
>> Dear users,
>>                 I am working with PTP1B protein. Recently I tried to 
>> run it in gromacs along with an inhibitor 
>> {[7-(DIFLUORO-PHOSPHONO-METHYL)-NAPHTHALEN- 
>> 2-YL]-DIFLUORO-METHYL}-PHOSPHONIC ACID    [FNP in short]. The problem 
>> is that  gromacs does not recognize  FNP and hence I am not able to 
>> generate a topology file of it using pdb2gmx. I tried using the The 
>> Dundee PRODRG server to generate the topology file with the pdb file 
>> as the input. The problem is that it does generate the topology file 
>> but without any hydrogens. Even the  polar hydrogens information is 
>> not available inspite of it being a part of my input pdb file. Thus I 
>> am not able to use FNP with the polar hydrogens for my runs.
>>
>> If anyone has faced similar problems please do help if you can.
>>
>> Thanking you,
>> Cheers.
> 
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