Hi, [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 > 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. -- ------------------------------------------------------ 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: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
