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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