AMBER Archive (2006)

Subject: Re: AMBER: working with large strained system

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Jul 06 2006 - 12:06:57 CDT

> I was hoping that someone could give me advice about
> AMBER's capabilities for working with a very big, very
> strained system. I have a system of about 23,000 heavy
> atoms (and it will be a lot bigger after I add
> explicit solvent). The system is not a simple crystal
> structure; we have actually performed some refinement
> procedures on it to test a hypothesized conformational
> change, and the resulting structure is rough, with a
> lot of atoms that are close together and things
> twisted in strange ways. I am hoping that an AMBER
> minimization can correct these problems with the
> structure.
 
You might want to consider using cartesian restraints to hold
the parts you believe in fixed, while running low-temperature
dynamics (10-100K) to untangle the rest. This after some
minimization. It can prevent some of the local strain from
distorting the rest of the structure as it relaxes.

Bill
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