AMBER Archive (2009)

Subject: Re: [AMBER] Timescales and restraints for protein-small ligands movement simulations

From: Vivek Sharma (vivek.viv.sharma_at_gmail.com)
Date: Sun Aug 02 2009 - 01:29:13 CDT

Hello,

I think that either you need to increase the ns(s) simulation to much much
longer durations to observe such a large movement OR you could also try
steered-molecular dynamics.

ViV

2009/8/1 Andrew Voronkov <drugdesign_at_yandex.ru>

> Maybe I should try REMD or several heating-cooling cycles?
>
> Best regards,
> Andrew
>
> 01.08.09, 10:23, "Andrew Voronkov" <drugdesign_at_yandex.ru>:
>
> > Dear Amber users,
> > I am very sorry if this is a kind of offtopic here, but it is related to
> simulations conditions too.
> > I want to simulate the crawl of 12 amino acid peptide on the surface of
> 124-amino acid domain of the receptor. I've got three alternative initial
> complex structures by protein-protein docking. I want to evaluate each of
> these initial complexes stability. Before making calculations of free energy
> by MM-PBSA I want to study the movement of these peptides on the surface of
> the receptor domain.
> > After molecular dynamics during 30 nanoseconds from each initial position
> with TIP3P waters using amber03 force field there seems to be no significant
> changes, no crawl on the surface of the receptor - only small conformational
> changes in the peptide structure.
> > Is 30 nanosecond timescale is too small to get any movement of such a
> small peptide on the surface of the small receptor domain?
> > Maybe I should add some additional constraints on the 124-amino acids
> domain, for which the x-ray structure is known?
> > Best regards,
> > Andrew
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