Thanks a lot Ran and Mark for your valuable suggestion. Warm regards, Tuhin
[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 _______________________________________________ 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 _______________________________________________ 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
