AMBER Archive (2006)

Subject: RE: AMBER: Radius of gyration

From: Andy Purkiss-Trew (a.purkiss_at_mail.cryst.bbk.ac.uk)
Date: Fri Nov 24 2006 - 13:34:52 CST

Hi Kepa,

I've just checked the source code for amber 8 and you are correct that
ptraj doesn't have support for radgyr. It might be worth asking the
AMBER people if it is possible to have a copy of the source for ptraj
from version 9. There used to be a version available for download from
Thomas Cheetham's website, but that is a 2003 version and doesn't have
the radgyr keyword either.

Andy

On Fri, 2006-11-24 at 18:45 +0100, kepa koldo burusco wrote:
> [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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-- 
Cat, n.: Lapwarmer with built-in buzzer.
+----------------------------------------------------------------------+
| Andy Purkiss-Trew, School of Crystallography,Birkbeck College,London |
|           E-mail   a.purkiss_at_mail.cryst.bbk.ac.uk                    |
|      Phone 020 7631 6869 (Work) or 07763 490 360 (Mobile)            |
+----------------------------------------------------------------------+

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