Hi Mannan,
Unfortunately in AMBER, no matter what, you need to create a prmtop for all
residues, even if they will be governed by quantum instead of molecular
mechanics. This may seem ridiculous at first since you will probably want
to ignore bonded and electrostatic terms during dynamics/minimization, but
non-bonded, non-electrostatic (*i.e. *Lennard-Jones) terms will probably
need to be present for QM/MM simulations and radii must be defined for
GB/PB simulations. The choice of these parameters is non-trivial and
non-standardized. I would suggest surveying the literature for the amino
acid in question.
If you simply want to do gas-phase QM calculations, then I would refer you
to the documentation for SQM in the AMBER Tools manual (although this does
not perform dynamics or saddle point searches at present).
Regards,
Brian
On Tue, Oct 9, 2012 at 9:24 AM, Mannan <malie_03.yahoo.co.in> wrote:
> Hi Amber peoples,
>
> I would like to use QM method to an unusal aminoacid, which is not in any
> libraries,
>
> What would be the best way to do it in an academic lab?
>
> Many Thanks in Advance,
>
> Mannan
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
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Received on Tue Oct 09 2012 - 09:00:07 PDT
