sonali dhindwal wrote:
--
Sonali Dhindwal
--- On *Sun, 21/3/10, sonali dhindwal /<[email protected]>/*
wrote:
From: sonali dhindwal <[email protected]>
Subject: query regarding pdb2gmx program for protein with metal and
a ligand
To: [email protected]
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.
Really? This error has been posted hundreds of times so it should be very easy
to find in the list archive. Furthermore:
http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database
Treating a transition metal is not a trivial problem. For instance:
http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species
Ligand parameterization is also a potentially (very) difficult task. See the
above link.
-Justin
Regards
--
Sonali Dhindwal
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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