Dear Carlos
thanks a lot for your quick response.
I agree with you, same prmtop works well for all low energy structure
minimization, I m still puzzled should I use rst files from MD (loops
md1...md10) or fresh inpcrd file for that particular low-energy (1 to 10
separate inpcrd file) structure.?
thanks in advance
Best wishes
Vince
On 20 December 2015 at 14:04, Carlos Simmerling <carlos.simmerling.gmail.com
> wrote:
> there is no reason to use a different prmtop for the minimization as
> compared to the one used for the MD, unless you changed something about the
> system after the MD (like removing the water, etc).
>
> On Sun, Dec 20, 2015 at 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 - 05:30:04 PST
