[gmx-users] Fw: query regarding pdb2gmx program for protein with metal and a ligand

[sonali dhindwal]

--
Sonali Dhindwal

--- On Sun, 21/3/10, sonali dhindwal <sonali11dhindwal at yahoo.co.in> wrote:

From: sonali dhindwal <sonali11dhindwal at yahoo.co.in>
Subject: query regarding pdb2gmx program for protein with metal and a ligand
To: mailman at gromacs.org
Date: Sunday, 21 March, 2010, 1:43 PM

Hello Sir/Madam,
I am new to Gromacs, and o want to run molecular dynamics study for analysis of my modelled protein which consist of a Metal Mn and a Ligand in it. 
But whenever I run the first step of generation of topology file through pdb2gmx  program, I am getting error msg that 
Fatal error:
Residue 'MN' not found in residue topology database

So, the program fails, and I cant move forward.
I tried by deleting metal and ligand from my protein, then it is working, but I have to consider Metal and ligand.
I searched on google also, regarding this error, but couldnt get through this problem, so please help.
Thanks in advance.

Regards
--
Sonali
 Dhindwal

       
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