Thank you very much Tsjerk. Actually I searched in google and somewhere i read that it might be because either the topology is bad or the starting structure has clashes that cannot be adequately addressed using EM or because of improper parametrization.
On Sat, Jul 16, 2016 at 3:43 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Swagata, > > That's not a problem. You should be fine running a simulation, given the > potential energy of the system. Check the archives for more elaborate > comments on this matter. And please check the archives/google before > posting questions. We like breaking our heads over new, tough issues, and > don't really fancy chewing on old matters, which come up on a monthly > basis. > > Cheers, > > Tsjerk > > On Jul 16, 2016 12:08 PM, "Swagata Patra" <swagatal...@gmail.com> wrote: > > > Hello evryone, > > > > I am tying to do simulation of a protein-ligand complex. But in energy > > minimization step I am facing the following problem: > > > > > > Stepsize too small, or no change in energy. > > Converged to machine precision, > > but not to the requested precision Fmax < 1 > > You might need to increase your constraint accuracy, or turn > > off constraints alltogether (set constraints = none in mdp file) > > > > writing lowest energy coordinates. > > > > Steepest Descents converged to machine precision in 37686 steps, > > but did not reach the requested Fmax < 1. > > Potential Energy = -1.22228866049133e+06 > > Maximum force = 1.60313450715092e+02 on atom 1628 > > Norm of force = 1.38085169243203e+00 > > > > i prepared the ligand topology file using ATB. There I was getting an > > warning like : "This molecule contains non-standard atom types not > included > > in the standard GROMOS 53A6 and 54A7 forcefield. To use these atom types > > the internal GROMACS parameter files must be updated. These can be > > downloaded using the link below. So I donloaded the filee and also modify > > it in topology file. > > > > Please help me to overcome the problem. > > I am attaching the topology file. > > > > -- > > Swagata Patra > > M.Tech (Biotech) > > JRF > > IIT Guwahati > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Swagata Patra M.Tech (Biotech) JRF IIT Guwahati -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
