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

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 23 14:07:07 CET 2010

sonali dhindwal wrote:
> --
> 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.

Really?  This error has been posted hundreds of times so it should be very easy 
to find in the list archive.  Furthermore:


Treating a transition metal is not a trivial problem.  For instance:


Ligand parameterization is also a potentially (very) difficult task.  See the 
above link.


>     Regards
>     --
>     Sonali Dhindwal
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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