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

[van Bemmelen]

Hi Soni,

I have never had such problems, but only some suggestions:
1) Try the PRODRG beta server
(http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta)
2) Try drawing your molecule (or part of it) directly with the JME
editor, included on the PRODRG website
3) Try using another input file type, e.g. MDL MOLfile

Hope it helps,
Jeroen


>Date: Thu, 10 Jan 2008 02:48:46 -0800 (PST)
>From: Mufaddal Soni <muffi_gro at yahoo.com>
>Subject: [gmx-users] Generating topology file for a molecule (FNP) not
>	in	the gromacs library.
>To: gmx-users at gromacs.org
>Message-ID: <959429.81481.qm at web44913.mail.sp1.yahoo.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>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.
>
>Soni Mufaddal Saifee,
>B.Tech IIT Madras.