AMBER Archive (2008)

Subject: Re: AMBER: about NMR refinement in explicit solvent

From: David A. Case (
Date: Thu Sep 11 2008 - 12:24:37 CDT

On Tue, Sep 09, 2008, Rogelio HernŠndez wrote:
> I am trying to optimize my protein structures obtained from
> CYANA but I have several doubts about the scripts I wrote to perform
> NMR refinement of structures in explicit solvent using AMBER 9.
> I am using TIP3P
> water model and amber 99 FF for protein atoms.

You should not use ff99 for proteins; consider using ff99SB.

> The trouble was I expected improve the RMSD between† energy minimized
> structures respect the CYANA structures but this was not the outcome, maybe
> the parameters that I entered were not good values.

There is no reason to suppose the quality of a structure refinement is
related to the RMSD spread in the resulting structures. You should
rather look at energetic and structural indices, as well as deviations
from the NMR restraints you impose.

> On the other side I want
> to know if there are another protocol that you suggest me to perform
> NMR refinement in explicit solvent because the last one takes about
> 120 h of CPU time per structure in a Pentium V processor.

There are not a lot of really "standard" protocols, especially for
explicit solvent refinements. You should try variants of basic
protocols, and see how much things change. Each protein (and
corresponding NMR data set) is unique.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)