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.