On Thu, Oct 22, 2015, Kumar cerm wrote:
> I have a novel peptide and is incorporated with non standard amino acid
> residues. I have already cracked all the possible steps to handle it
> in AMBER and now I have obtained preliminary structure with the NOE
> violation of 0.2-0.7 A* (200 noes + 20 hydrogen bonds). But my system
> visually looks 70% close to the expected structure but I would like to
> improve it. Currently I have annealed my system with noe, hydrogen
> bond restraints in vacuum.
I would recommend using igb=8 along with the ff14SBonlysc force field. As
always, take care to tweaking things just to get the "expected structure".
> 2) Is it possible to perform annealing in TIP3BOX.
Yes. Often, one uses a lower top temperature in explicit solvent. I don't
know if this is related to the problems you have had or not.
....dac
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Received on Sat Oct 24 2015 - 06:00:03 PDT
