AMBER Archive (2005)

Subject: Re: AMBER: Sander minimization & dynamic question

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Apr 04 2005 - 06:48:26 CDT


you may want to include restraints from the NMR data in your simulations,
or at least verify that the final structures still are consistent with
that data.

chaiann ng wrote:

> Dear Amber User:
>
> I would like to hear some opinions from you guys about my method below.
>
> I am doing modeling using NMR spectroscopy to obtain NOE constraints,
> and obtain intial structure from CYANA. What I want to achive is
> include the solvent in minimization and dynamic explicitly. My steps are:
> 1. Min1, Min2, MD1, MD2 */Running Minimisation and MD (in explicit
> solvent)/*(http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/section5.htm)
>
> 2. from MD2, I identify the 20 lowest energy structures from 500
> structures (20ps-120ps) without the solvent present.
>
> 3. I redo the Min1 and Min2 with solvent at those 20 structures. That
> would be my final 20 structures for publication.
>
>
> My questions and concerns are:
>
> 1. With explicit solvent, the dynamic can only be at room temperature.
> Am I
> correct?(http://amber.scripps.edu/tutorial/dna_NMR/nmr_dna_tutorial.htm)
>
> 2. Is there any problem with my method? Any suggestions?
>
>

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