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

[Chris Neale]

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.