AMBER Archive (2003)

Subject: Re: AMBER: Protein Rotation

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Nov 11 2003 - 09:11:40 CST

some rotation of a solute is expected, but it should not
rotate "too much" in explicit solvent. rigid body motion of
the system as a whole is removed when you use the NSCM
namelist variable. however, I don't think that you want to
remove all solute rotation during MD just to help
the analysis. what you should do is to remove it during
the RMSD calculation.

if you want to get the residue RMSD values, then
the frames should be fit to a reference structure
first. you should be able to do this in carnal, but
ptraj will also do it. I use my moil-view program
for per-residue RMSD values and it fits to a reference
frame first so rotation has no effect.

maybe someone more familiar with carnal can say
if it performs a best-fit prior to residue RMSD calculation.
Carlos

----- Original Message -----
From: <Frederico.Miranda_at_ibmb.uib.no>
To: <amber_at_scripps.edu>
Sent: Tuesday, November 11, 2003 9:52 AM
Subject: Re: AMBER: Protein Rotation

> 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.
> > >
> >
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> >
> >
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>
>
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