[gmx-users] CHARMM36 force field available for GROMACS

[CHEN Pan]

Dear Justin,

Thanks for you information.
I have a small query on the residue name in the "charmm36.ff" folder. Is
there any document illustrating for the corresponding full name of residues
in the ".rtp" file.
As you have illustrated in the file "forcefield.doc", the parameters for
some carbohydrates such as glucose should be implemented. I found the
residues named "AALT" or "AALL" should be for glucose, but the names are
not easy to understand. Is there any illustration already existing to
explain what the abbreviations stand for?

Pan


2013/10/9 rajat desikan <rajatdesikan at gmail.com>

> Superb stuff, Justin. Thank you so much. Is it asking too much for a brief
> list of the test systems that you used? Thanks again.
>
>
> On Wed, Oct 9, 2013 at 1:46 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> > All,
> >
> > I am pleased to announce the immediate availability of the latest
> CHARMM36
> > force field in GROMACS format.  You can obtain the archive from our lab's
> > website at http://mackerell.umaryland.**edu/CHARMM_ff_params.html<
> http://mackerell.umaryland.edu/CHARMM_ff_params.html>
> > .
> >
> > The present version contains up-to-date parameters for proteins, nucleic
> > acids, lipids, some carbohydrates, CGenFF version 2b7, and a variety of
> of
> > other small molecules.  Please refer to forcefield.doc, which contains a
> > list of citations that describe the parameters, as well as the CHARMM
> force
> > field files that were used to generate the distribution.
> >
> > We have validated the parameters by comparing energies of a wide variety
> > of molecules within CHARMM and GROMACS and have found excellent agreement
> > between the two.  If anyone has any issues or questions, please feel free
> > to post them to this list or directly to me at the email address below.
> >
> > Happy simulating!
> >
> > -Justin
> >
> > --
> > ==============================**====================
> >
> > Justin A. Lemkul, Ph.D.
> > Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu>
> |
> > (410) 706-7441
> >
> > ==============================**====================
> > --
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>
> --
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
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Pan Chen
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