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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Received on Mon Apr 04 2005 - 12:53:01 PDT
