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+' 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 Anyway I cannot consider "calcium ion" as ligand right? * Regards** N.T. Devika* On Wed, Jan 16, 2013 at 5:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/16/13 5:32 AM, Devika N T wrote: > >> 4.5.5 versio >> >> Writing topology >> Processing chain 2 'A' (4 atoms, 4 residues) >> Warning: Starting residue CA149 in chain not identified as >> Protein/RNA/DNA. >> Warning: Starting residue CA150 in chain not identified as >> Protein/RNA/DNA. >> Warning: Starting residue CA151 in chain not identified as >> Protein/RNA/DNA. >> Warning: Starting residue CA152 in chain not identified as >> Protein/RNA/DNA. >> Problem with chain definition, or missing terminal residues. >> This chain does not appear to contain a recognized chain molecule. >> > > Note what the following line tells you: > > > If this is incorrect, you can edit residuetypes.dat to modify the >> behavior. >> >> >> > So pdb2gmx is recognizing "CA" (calcium?) as some unknown type. This may > or may not be relevant for your purposes. The topology should have been > written just fine as long as the parent force field recognizes CA. If it > is an ion, do as pdb2gmx suggests and add this information to > residuetypes.dat, which will make default group generation easier later on. > > -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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
