I believe ptraj should be able to do that.
Cheers,
Gustavo.
P.S.: It would be best if you started a whole new thread, since this
is a different subject. Instead of hitting "reply" to an old message,
send a new e-mail directly to amber.scripps.edu (see the footer
autimatically added attached to all messages). If you hit reply, as
you probably did this time, chances are that very few people are going
to see your message. Most will just think it's part of a thread they
are not following, and you won't get as many useful answers as you
want.
On 1/30/07, santanu roy <66.santanu.gmail.com> wrote:
>
> Hi,
> Is there any method in amber which can calculate RMSD of atoms/residues
> just from any pdb file,
> I mean to say , I want to plot RMSD Vs atoms/residues from crystallographic
> structure and to compare it with the rmsd plot got from the simulation. It
> will be a good comparision if we plot both of them in one place.
> Regards
> Santanu
>
>
>
>
> On 1/29/07, Gustavo Seabra <gustavo.seabra.gmail.com> wrote:
> >
> > On 1/29/07, santanu roy <66.santanu.gmail.com> wrote:
> > >
> > > Sir ,
> > > I am done with my qm/mm simulation , and have got expected
> result.
> >
> > Glad to hear that!
> >
> >
> > > Anyway , I have some basic questions regarding AMBER tutorial one ,
> > > simulation of DNA in solvated form.
> > > [...]
> >
> > I'd suggest that you open a new thread with this one, since it's a
> > different topic altogether.
> >
> > Good luck,
> >
> > Gustavo.
> >
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> >
>
>
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Received on Wed Jan 31 2007 - 06:07:37 PST
