[gmx-users] Mg ion not recognize.

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 13 06:34:45 CEST 2009

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.


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