I'm working with Amber 7 and I'm using a periodic calculation. There is no
restrictions on the protein nor frozen parts. If you need more information
just tell me.
Thank you for help.
Quoting Carlos Simmerling <carlos.csb.sunysb.edu>:
> 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.ibmb.uib.no>
> To: "AMBER Reflector" <amber.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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Received on Tue Nov 11 2003 - 15:53:01 PST
