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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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