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. Best, Tuhin _______________________________________________ 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
