AMBER Archive (2006)

Subject: RE: AMBER: Radius of gyration

From: kepa koldo burusco (kepaquestions_at_yahoo.es)
Date: Fri Nov 24 2006 - 11:45:55 CST

[24-XI-2006]

Hi Andy,

I've just checked the amber7, amber8, and amber9
versions of ptraj manuals. You were right when you
said that it calculates both the parameters but... I
still have doubts. I mean, amber9-ptraj really
calculates RMSD and Radius of Gyration. Nevertheless,
apparently, amber8-ptraj and amber7-ptraj are only
able to calculate RMSD.

We usually work with amber7, and I was wondering... Is
it really true that amber7 and amber8 versions of
ptraj cannot calculate radius of gyration? Or maybe it
was ommited in the manual but still they were able to
do that?

Any help??? I'm really interested, because we work
with amber7!!!

Thank you very much in advance...

Kepa K. Burusco

PhD Student
Universidad Autónoma de Barcelona
BARCELONA (Spain)

###################################################

 --- Andy Purkiss-Trew
<a.purkiss_at_mail.cryst.bbk.ac.uk> escribió:

> Hi Rosajann and Kepa,
>
> ptraj is able to calculate radius of gyration, as
> well as rmsd. See the
> keyword radgyr in the manual. It can also calculate
> the radius of
> gyration for part of the molecule, using masks.
>
> The atomicfluct option may also be of interest when
> looking at per
> residue fluctuations of the protein.
>
> Hope this is of help
>
> Andy

        
        
                
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