AMBER Archive (2006)

Subject: Re: RE: AMBER: Radius of gyration

From: Elijah Gregory (ejgregory_at_gmail.com)
Date: Fri Nov 24 2006 - 14:33:50 CST

I was wondering what the message said other than something about
receiving a concrete answer and something about 'interest in'
something else. I think ptraj is generally offered freely separate
from AMBER, but I could be wrong. Tom, is this up yet?

~Elijah

On 11/24/06, Andy Purkiss-Trew <a.purkiss_at_mail.cryst.bbk.ac.uk> wrote:
> Actually, (to answer your personal comment to Kepa, which has gone to
> the whole list) I think that the question is of general interest to the
> AMBER community.
>
> And in that vein, do you not think it is polite to send a question in
> english, as well as Spanish to an English mailing list!!
>
> On Fri, 2006-11-24 at 19:25 +0100, Carles Jaime Cardiel wrote:
> > kepa,
> > Si respondes a alguien en concreto, no crees que no deberías enviarlo a la lista sino al interesado?????
> > Un saludo,
> > Carlos.
> > ----------
> > Carlos JAIME
> > Catedràtic de Qca. Orgànica i Delegat del Rector per al Doctorat
> > Dept. Química, Fac. Cièncias (Cn)
> > Univ. Autònoma Barcelona
> > 08193 Bellaterra (Barcelona)
> > SPAIN
> >
> > ----- Missatge original -----
> > De: kepa koldo burusco <kepaquestions_at_yahoo.es>
> > Data: Divendres, Novembre 24, 2006 6:45 pm
> > Assumpte: RE: AMBER: Radius of gyration
> >
> > > [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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> --
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> +----------------------------------------------------------------------+
> | 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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