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

Ran Friedman r.friedman at bioc.uzh.ch
Thu Jun 12 09:27:34 CEST 2008


tuhin at iitk.ac.in 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
> 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 ?
It's not always sufficient. Check e.g. J. Comput. Chem. 29:1163-1169, 2007.
Whatever parameters you're using, check the location of the ion
carefully and try to match any available experimental data.
> 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
This sounds reasonable.


Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman

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