[gmx-users] Facing poblem in enegy minimization step

[Swagata Patra]

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 <tsjerkw at 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" <swagataliza at 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
> >
> > --
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-- 
Swagata Patra
M.Tech (Biotech)
JRF
IIT Guwahati