Just go to NCBI and in the PubMded input Amber and see
what you will get.
For the MM/PBSA work for energy calculation, I would
rather recommend you to do a calorimetry assay because
the calculation cannot give you all the information.
Best regards.
Fenghui Fan
--- "Hu, Shaowen (JSC-SK)[USRA]"
<Shaowen.Hu-1.nasa.gov> wrote:
> Thanks a lot. My computational resource will allow
> me to run thus far.
> Could you refer any papers that have done with
> similar systems? How will
> the MM/PBSA work for energy calculation?
>
> Best,
>
> Shaowen Hu
>
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf
> Of Fenghui Fan
> Sent: Tuesday, February 20, 2007 10:53 PM
> To: amber.scripps.edu
> Subject: Re: AMBER: Is this system too large?
>
> I think it can work. But you may have your
> productive MD a little
> longer, for example 5 ns.
>
> Best regards.
>
> Fenghui Fan
>
>
> --- "Hu, Shaowen (JSC-SK)[USRA]"
> <Shaowen.Hu-1.nasa.gov> wrote:
>
> > Dear All,
> >
> > I am a novice to AMBER. After running some
> tutorials from your
> > website, I tried my first project with AMBER 9. I
> am just wondering
> > whether somebody can give me some ideas on the
> suitability of this
> > system. If it is beyond the capability of AMBER, I
> may switch to other
>
> > smaller ones.
> >
> > The complex is composed of a protein heterodimer
> > (1023 amino acids) and a 14-mer DNA. After added
> in oct water with
> > least edge distance 8.0, it has
> > 137451 total atoms. I am afraid that it may be too
> large to get
> > reasonable comformational analysis and energetical
> analysis ( like the
>
> > MM/PBSA scheme).
> >
> > Thanks a lot,
> >
> > Shaowen Hu
> >
> >
>
>
>
>
>
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Received on Sun Feb 25 2007 - 06:07:11 PST
