[gmx-users] Ca2+ forcefield and Temp-coupling

tuhin at iitk.ac.in tuhin at iitk.ac.in
Thu Jun 12 08:44:04 CEST 2008

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
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 ?

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

I would really appreciate any suggestion.

Thank you for your precious time.


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