AMBER Archive (2006)

Subject: AMBER: How to simplify this big system rationally to perform MD studies

From: Zhihong Yu (computation_at_mail.nankai.edu.cn)
Date: Wed Jun 14 2006 - 05:43:59 CDT

Dear all,

    Herein I'm asking a nontechnical question. I want to perform MD studies comparatively on a wild-type and single point mutant enzyme including inhibitor, the system is a homodimer and the inhibitor is located between the interface of the two monomers, the mutated residue is within 6 angstrom of the inhibitor. Because the monomer consist of nearly 650 residues, the solvated system will include about 140000 atoms, which is too big system to run MD considering my own computational power. So I want to get some advice from amber list members to rationally simplify this study case, any suggestion will be greatly appreciated! thanks in advance!

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