AMBER Archive (2003)

Subject: Re: AMBER: Protein Rotation

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Nov 11 2003 - 07:02:32 CST

you must give more details when you ask for help.
What version of AMBER are you using?
Is this a periodic calculation, is it gas phase,
is it GB solvation?

Carlos

----- Original Message -----
From: <Frederico.Miranda_at_ibmb.uib.no>
To: "AMBER Reflector" <amber_at_scripps.edu>
Sent: Tuesday, November 11, 2003 7:47 AM
Subject: AMBER: Protein Rotation

>
> Hye, I made a MD simulation for a protein, and used carnal to determine
RMS
> for each residue, but my protein is rotating during the MD, so I have a
great
> discrepancy in the values. Is there a way that I could remove the effect
of
> the rotation when doing the calculation?
>
> Thank you.
>
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