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

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 10 13:18:39 CET 2008

Quoting Mufaddal Soni <muffi_gro at yahoo.com>:

> Dear users,
>                  I am working with PTP1B protein. Recently I tried to run it
> in gromacs along with an inhibitor
> 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.

I know that PRODRG (which I believe uses the old ffgmx) does not add aromatic
hydrogens to molecules, but the PRODRG beta site (which uses GROMOS96) does. 
You may want to try the beta server, since ffgmx is deprecated (as noted in the


> Thanking you,
> Cheers.
> Soni Mufaddal Saifee,
> B.Tech IIT Madras.
> ---------------------------------
> Be a better friend, newshound, and know-it-all with Yahoo! Mobile.  Try it
> now.


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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