[gmx-users] Mg ion not recognize.

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Apr 13 09:47:28 CEST 2009


Mg is probably in the force field already. You don't need to run it
through pdb2gmx. Add it manually after generation of the topology for
the protein. #include "ions.itp" in the topology file and add the
correct name (check ions.itp) under [ molecules ]. Be sure to have all
atoms matching in order with your coordinate file.



On Mon, Apr 13, 2009 at 6:34 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> akalabya bissoyi wrote:
>> "hello gromacs,
>> i am trying to simulate my protein ligand complex but my protein contains
>> Mg ion and while running Gromacs error is coming in command pdb2gmx.It is
>> not able to recognize Mg ion.
>> I included the coordinates for Mg ion in protein pdb file.And when i
>> included coordinates for Mg ion in ligand file , Prodrg server was showing
>> error during generation of ligand toplogy file as it doesnt include Mg ion.
>> So pls suggest me how can i do this job.."
> There is probably no straightforward clearly-correct approach. See
> http://wiki.gromacs.org/index.php/Exotic_Species in the first instance.
> Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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