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

Mufaddal Soni muffi_gro at yahoo.com
Thu Jan 10 11:48:46 CET 2008

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,

Soni Mufaddal Saifee,
B.Tech IIT Madras.

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