Thank you Justin for your valuable suggestion. I will follow it up.
* Regards** N.T. Devika* On Wed, Jan 16, 2013 at 6:16 PM, Justin Lemkul <[email protected]> wrote: > > > On 1/16/13 7:38 AM, Devika N T wrote: > >> Thank you Justin for your reply. >> >> I need to perform the effect of Calcium (CA) with protein Calmodulin. >> >>> From the warning message its clear that "CA" is not identified as ion. >>> >> But previously I tried the run with Gromacs version 4.0.7 at that time >> >> Version 4.0.7 >> >> >> Warning: 'CA' not found in residue topology database, trying to use 'CA2+' >> Warning: 'CA' not found in residue topology database, trying to use 'CA2+' >> Warning: 'CA' not found in residue topology database, trying to use 'CA2+' >> Warning: 'CA' not found in residue topology database, trying to use 'CA2+' >> >> > This only implies that the name is wrong with respect to what the .rtp > file expects. > > > So I thought in version 4.5.5 it will have the residuetype.dat file >> updated >> with calcium. >> Fine let me try by adding calcium to residuetypes.dat >> >> > That should be the solution. > > > Anyway I cannot consider "calcium ion" as ligand right? >> >> > You can consider it however you like, but if you're interpreting a ligand > to be something for which you need a topology from an external source, then > no. All Gromacs force fields have parameters for calcium and should be > processed automatically by pdb2gmx. In fact, I just checked > residuetypes.dat and there is a line indicating CA as an Ion, so there > should be no problem at all. Looking more closely at the pdb2gmx output > from your original post, all that is indicating is that there is a species > that is not Protein/DNA/RNA, which in this case is of course what one would > expect. There is no problem whatsoever. > > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
