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

[Mark Abraham]

On 23/03/2010 10:43 PM, sonali dhindwal wrote:

See 
http://www.gromacs.org/Documentation/How-tos/Parametrization#Exotic_species

Mark

> --- 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.