Dear David
Good evening...
Many thanks for yous response.
Yes, I have tried to perform annealing on my system in TIP3PBOX with
restraints, but I haven't restricted the temperature, I will give a try
with lower temperature.
I have tried GB model with igb=2 but there was no much improvement in the
structure, I will try with igb=8.
Again, thank you so much for your suggestions..
Best regards
Vince
On 24 October 2015 at 14:34, David A Case <dacase.scarletmail.rutgers.edu>
wrote:
> 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 - 17:00:04 PDT
