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 Sat Nov 21 2015 - 18:00:03 PST
