[AMBER] 10 Lowest energy structures from GB ==>Explicit solvent refinement

From: V. Kumar <vin.vasanth.gmail.com>
Date: Sat, 21 Nov 2015 16:25:37 +0100


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.

Thank you in advance..

Have a nice week end

Best wishes
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Received on Sat Nov 21 2015 - 07:30:03 PST
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