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
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Received on Thu Oct 07 2010 - 11:00:03 PDT
