Thanks a lot.
Regards,
Soumya
On Thu, Oct 7, 2010 at 11:18 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> it depends on what you want to know. if you want the change in the internal
> structure of the loop, use the loop residues only. if you want the rmsd of
> the loop with respect to the protein, fit the protein with an rms command
> (no loop) and then do another rms command with loop residues only and say
> "nofit". the syntax is in the manual.
> which of these you want to do depends on what you want to klearn- there
> isn't a right or wrong answer. you need to think about what is being
> measured and what you want to know.
>
>
> On Thu, Oct 7, 2010 at 12:55 PM, Soumya Lipsa Rath
> <soumyalipsabt.gmail.com>wrote:
>
> > Dear Amber Users,
> >
> > I have to calculate the RMSD of a loop of protein.
> > For the ptraj commant *'rms'* the manual says; *"This will RMS fit all
> the
> > atoms in the mask based on the current mode"*.
> > My doubt is whether to exclude those loop residues and include all
> others?
> > If so will it give the RMSD values for that loop?
> >
> > Regards,
> >
> > Soumya
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 07 2010 - 21:00:04 PDT
