AMBER: Sander minimization & dynamic question

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From: chaiann ng <andy810915.hotmail.com>
Date: Mon, 04 Apr 2005 18:45:48 +0800

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?

Download your favorite songs at MSN Music - Over 1 million songs for just 99¢ each ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu Received on Mon Apr 04 2005 - 11:53:01 PDT