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

From: David A Case <>
Date: Sat, 21 Nov 2015 20:34:08 -0500

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").


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Received on Sat Nov 21 2015 - 18:00:03 PST
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