Dear David
Thank you so much for your suggestions.
Best wishes
Vince
On Nov 22, 2015 2:34 AM, "David A Case" <david.case.rutgers.edu> wrote:
> On Sat, Nov 21, 2015, V. Kumar wrote:
> >
> > I have just finished IGB=5 simulated annealing (10ns, loops of 200ps).
> Now
> > I have 10 best lowest energy structure. Now I have to go in to refinement
> > steps in explicit solvent with NMR restraints on.
> >
> > My question is, do I have to perform refinement of each low energy
> > structure separately or do I have to combine 10 structure into one pdb
> file
> > and create solvated prmtop/inpcrd. In the paper people have mentioned "
> > Lowest-energy structures from GB calculations underwent further MD
> > refinement in explicit solvent " and I dont know whether 10 structure
> > refinement together or one by one refinement.
>
> You want to do an explicit solvent simulation for each of the ten GB
> structures, that is ten solvated refinements ("one by one").
>
> ....dac
>
>
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Received on Sun Nov 22 2015 - 04:30:07 PST
