Thanks Dwight, I'll take a look at nab, sound like an option.
To Everyone: I cannot find a section of nmode on the Amber11 and AmberTools
1.4 User's Manual.
Where can I find good nmode documentation?
David
On Tue, Jun 7, 2011 at 8:07 PM, Dwight McGee <dwight.mcgee.gmail.com> wrote:
> Hi,
>
> *nmode* can be used to perform a normal mode analysis but I would suggest
> instead using *nab*. The nab section in the AmberTools 1.5 manual has an
> example of how to write such a script. You can also take look at mmpbsa.py
> nab program which is in the mmpbsa_py folder in the AmberTools directory as
> an example. Hope that helps.
>
> On Tue, Jun 7, 2011 at 7:08 PM, David Cantu <cantudav.gmail.com> wrote:
>
> > Dear Amber users/developers,
> >
> > I want to do a normal mode analysis of a small protein using nmode in
> > Amber.
> > However, I cannot find much documentation about nmode in Amber. Are there
> > any documents or useful links?
> >
> > Can normal mode analysis of a small protein be done using nmode in Amber?
> >
> > Thank you,
> >
> > David
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> Graduate Student
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
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Received on Wed Jun 08 2011 - 08:30:03 PDT
