Dear Carlos
thanks a lot for your answer, its clear to me now.
best wishes
Vince
On 20 December 2015 at 15:44, Carlos Simmerling <carlos.simmerling.gmail.com
> wrote:
> I'm not sure I understand. If your goal is to minimize the final structure
> from md, use the final rst file as the inpcrd. If the goal is to minimize
> the low energy snapshots,use those as inpcrd. I don't think energy analysis
> of snapshots in explicit water is very meaningful though. The water
> introduces significant noise to the snapshot energies. In any case,the same
> prmtop can be used for all snapshots.
> On Dec 20, 2015 7:23 AM, "V. Kumar" <vin.vasanth.gmail.com> wrote:
>
> > Dear AMBERist
> >
> > I planing to perform minimization after simulated annealing ( 200ps*50
> > loops = 10ns). Visual inspection of my low energy structures extracted
> from
> > trajectory shows that there are still some strains on the side chains. I
> > already performed minimization that removed the strain. But I am not sure
> > that I did it in correct way (protocol).
> >
> > I have 50 sets(loops) of 200 ps simulated annealing MD data in explicit
> > solvent using NMR restraints during simulation. As per the low energy
> > search I found 10 structures from the different "md" sets. For eg. I have
> > md1, md2, md3, ...md50. I picked low energy structures lets say from
> md34,
> > md47, md50, few more.
> >
> > Now my question is I have same ".prmtop" for all strucuture, but I have
> > different ".rst" files. For eg. md1.rst, md2.rst, ......md50.rst. So to
> > minimize above 10 structure, for each model I constructed again new
> > ".prmtop and .inpcrd" and then I performed minimization in usual way. I
> > dont know its a correct way to do it.
> >
> > I also got another idea to use same prmtop but respective rst files to
> > minimize all 10 structures. I clearly dont know which method is correct.
> So
> > kindly request your suggestion and comments.
> >
> > thanks in advance..
> >
> > Have a nice weekend
> >
> > Best wishes
> > VINCE
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> >
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Received on Sun Dec 20 2015 - 07:30:03 PST
