Re: AMBER: Offending restraints????

From: David A. Case <case.scripps.edu>
Date: Tue, 26 Jun 2007 09:37:21 -0700

On Tue, Jun 26, 2007, saccenti.cerm.unifi.it wrote:
>
> These values come for experimental NMR restrains that have been randomly
> perturbed.

Does it really make sense to have perturbations that then give upper bounds
between non-bonded atoms of 1.2 Ang? I think you will just get horrible
energies and very unstable simulations.

You might try using the -ual option to makeDIST_RST: that will use the lower
bounds you provide, rather than assuming a default lower bound.

...dac

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Received on Wed Jun 27 2007 - 06:07:38 PDT
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