AMBER Archive (2009)

Subject: Re: [AMBER] About the croase grainded FF

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Feb 24 2009 - 02:40:53 CST

Hi Wang,

I guess at the moment you would need to implement it yourself. You need
to create libraries (off or mol2) for all residues you have in a coarse
grain force field. Than, you need to create an amber-like parameter file
to define the coarse grain particles, the bond lenghts, angles,
torsions, lennard-jones and so on ...

Then you need to make sure that the specifics of the coarse grain force
field can be accommodated in the AMBER options.
Maybe you'll need to define an additional force field equation as well
... Pay attention especially at the Lennard-Jones parameters. I don't
know how easy is this in AMBER ...

Once you have this, you can give it a try. I don't know which force
field you would like to use, but if it is MARTINI, then for the moment
you'd be better off using GROMACS for that, as it was developed for
GROMACS using GROMACS ...

Otherwise, I guess at a point in the future, AMBER will also acquire
this capability ...

Vlad

James W wrote:
> Dear all,
> Could you tell me how to run CG simulation in Amber ?
> Thanks
>
> Y.T Wang
>
> --
> National Center High-performance Computing (http://www.nchc.org.tw)
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> 

-- 
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Dr. Vlad Cojocaru

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Fax: ++49-6221-533298

e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

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