AMBER Archive (2003)

Subject: Re: AMBER: Protein Rotation

From: Frederico.Miranda_at_ibmb.uib.no
Date: Tue Nov 11 2003 - 08:52:44 CST

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_at_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_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.
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> >
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu