AMBER Archive (2009)

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

From: Andrew Voronkov (
Date: Sat Aug 01 2009 - 09:14:49 CDT

Maybe I should try REMD or several heating-cooling cycles?

Best regards,

01.08.09, 10:23, "Andrew Voronkov" <>:

> 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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