AMBER Archive (2008)

Subject: Re: AMBER: NMR structure as initial structure

From: David A. Case (case_at_scripps.edu)
Date: Tue Aug 05 2008 - 19:09:25 CDT

On Mon, Aug 04, 2008, Siddharth Rastogi wrote:

> I have to do Molecular dynamics of a protein (whose NMR structure is
> recorded at pH=4.5 and T=32 C.)
> Whether I can use directly that as the initial structure to run simulation
> or I have to maintain pH constant that is (pH=4.5) and run the simulation.

Unless you are very experienced with Amber (and MD simulations) already,
you should not attempt constant pH simulations.

You can use a variety of sources to get starting coordinates. What
residues you choose to protonate depends mainly on what conditions you
wish to simulate. The experimental structure probably had all
histidines protonated, and maybe some carboxylates as well. But trying
to match that only makes sense if you are interested in the properties
of your protein at pH 4.5. There are a variety of tools on the web
(e.g. pdb2pqr, H++,) that can be used to suggest protonation states
appropriate to given external conditions.

...good luck....dac

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