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

Jochen Hub jhub at gwdg.de
Thu Jan 10 16:06:12 CET 2008

Mufaddal Soni wrote:
> Dear users,
>                  I am working with PTP1B protein. Recently I tried to 
> run it in gromacs along with an inhibitor 
> 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.
Have you read
http://wiki.gromacs.org/index.php/Exotic_Species ?

Note however, that parametrizing some exotic molecule is a non-trivial 

Good luck, Jochen

> Thanking you,
> Cheers.
> Soni Mufaddal Saifee,
> B.Tech IIT Madras.
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Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de

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