AMBER Archive (2007)

Subject: Re: AMBER: Offending restraints????

From: David A. Case (case_at_scripps.edu)
Date: Tue Jun 26 2007 - 11:37:21 CDT

On Tue, Jun 26, 2007, saccenti_at_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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