AMBER Archive (2004)

Subject: Re: AMBER: target rmsd

From: Viktor Hornak (
Date: Mon Sep 13 2004 - 17:15:56 CDT

Dear Bill,

William Andrew McLaughlin wrote:
> Thank you for the help: I set nmropt=1 and reformated as prescribed. The
> rmsd during the simulation does then vary appropriately. FYI I changed
> the tgtmdfrc from 1 to 5000 and there is no energy barriers that appeared
> not to be overcome.
5000 seems excessively high and may lead to distorted structures or
simulation instability. I'd try to keep restraint force below 10 or so...

> Also, FYI I am using the function to do sampling of
> possible backbone conformations with a structure solved through X-ray
> crystallography. Since the function can be applied to non nmr structures
> would it be more appropriate to not have it as and nmr option? Also, for
I am not sure I understand what you're asking here. If you are concerned
about using 'nmropt' flag, you don't need to be - the name of the flag
doesn't mean you have to use nmr refined structures (it just indicates
that, historically, that's how it was used most often).

> this purpose, would a program like MOIL be more appropriate?
I never used MOIL and thus cannot comment on its usage...


Viktor Hornak
Center for Structural Biology   Phone: (631)632-1439
SUNY at Stony Brook             Fax:   (631)632-1555
Stony Brook, NY 11794-5115      E-mail:
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