Hi Tuhin, It depends on what you do. In both cases you will have to run grompp with an index file with a group specified, containing both the Protein and the calcium ion. You can take an existing index file (created simply with "echo q | make_ndx -f mystructure.gro") and add the number of the calcium ion under the label [ Protein ] or you make the combination within make_ndx, combining the two groups. In the later caseyou're likely to end up with a group called Protein_CA2+. Key issue to understand is that it's not sufficient to only define a group in the .mdp file. Except for the standard groups gromacs knows, a group will have to be defined through an index file.
Cheers, Tsjerk On Thu, Jun 12, 2008 at 10:08 PM, <[EMAIL PROTECTED]> wrote: > Dear Mark, > > To continue further, do I need to define my "energy groups" as: > > energygrps = Protein_CA2+ SOL > > OR, I could do as: > > energygrps = Protein SOL > > Best, > 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 [email protected] > 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 [email protected] > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] 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
