AMBER Archive (2004)

Subject: Re: AMBER: Close contact warnings

From: David A. Case (case_at_scripps.edu)
Date: Thu Feb 19 2004 - 10:30:15 CST

On Thu, Feb 19, 2004, L Jin wrote:

> I tried to use ntr=1 to restrain the HO and O connecting to it during
> minimizaiton. The result of the minimization seemed good. And the optimized
> structure looks good.

Yes, but this does not really do anything to keep the proton from getting
close to one of the other sulfate oxygens. You will need to look at the
structures when they fail in md to see if this is really the problem, and
then either change your force field parameters or use some other method
to keep these bad contacts (if that is indeed the problem) from forming.

..dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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