[gmx-users] Ca ion simulation incorporated in protein structure

Justin Lemkul jalemkul at vt.edu
Thu Aug 16 21:02:20 CEST 2012

On 8/16/12 2:45 PM, ram bio wrote:
> Dear Gromacs Users,
> I am trying to simulate a modeled protein -ligand complex in lipid
> bilayer using Gromacs 4.5.4 with Charmm27 FF. For my project purpose
> which is to see the effect of substitution of ions (Ca instead of Na
> ions) in the protein structure on protein ligand interactions ,  I
> have modeled the protein with Ca ions in the protein instead of Na
> ions. For the same, I was wondering if Gromacs 4.5.4 with Charmm27 FF
> can simulate Ca ions if incorporated in the protein instead of Na ions
> as i described here.

Check the ions.itp file in the charmm27.ff folder in $GMXLIB.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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