Dear Tsjerk, Actually, I have defined the groups for Temp-coupling as:
tc-grps = Protein_CA2+ SOL Thus, I felt would I be incorporating any errors, if I define my energygrps as: energygrps = Protein SOL I have generated my index.ndx file exactly the way you defined (Protein_CA2+) and supplied it to the grompp. Thanks for your valuable time. Regards, Tuhin > 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 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 >> > > > > -- > 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 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
