[EMAIL PROTECTED] wrote:
Dear Gromacs users,
My protein is a heterodimer (a small chain:A and a large chain:B). A
single Ca2+ ion is found interacting with residues from chain:B only. In
the .pdb file the Ca2+ is assigned a chain:B identifier.
HETATM 6504 CA CA B1579 23.021 -16.233 6.204 1.00 7.96 CA
When I visualize the protein and generate a conolly surface, I could see
the Ca2+ ion completely buried within chain:B. Now, I have two questions:
1. I would like to perform an MD on the above protein using Gromacs 3.2.1
Unless you have a really good reason (e.g. compatibility with old
results), you should be planning to use a more recent version.
suit with ffG43a1 forcefield. I know the Ca2+ ion is not accessible to
solvent molecules. Will the forcefield parameter for Ca2+ sufficient
enough to take this fact into account. I mean, Ca2+ in solvent and Ca2+ in
protein; for both the cases could I use the Ca2+ with +2 charge ? What
about the vdw contribution between the interacting residues from chain:B
and Ca2+ ion ?
To answer that, you should read about how these parameters were
developed for the force field. Perhaps you will need to refine them
yourself - but this is not a good thing to do early in your MD and/or
GROMACS experience.
2. When defining groups for Temp-coupling; could I do something like (as I
know the Ca2+ not accessible to solvent):
tc-grps = Protein_CA2+ SOL
That would be reasonable and effective.
Mark
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