DFTB parameters are maintained separately from AMBER at dftb.org. That is
the definitive site for what you can and cannot do with DFTB. However, the
AMBER implementation is also not up to date in terms of implementing the
full DFTB3 type Hamiltonian and this is the form most new parameter sets
are being developed for.
MM models for divalent metal ions are still a VERY active are of research
(I think I've seen at least two papers on model development in JCTC in the
last 3 months). I doubt force field files are available as part of the
AMBER distribution just yet, but you can probably get them from the authors.
Regards,
Brian
On Fri, Nov 15, 2013 at 11:30 AM, Thomas Exner <thomas.exner.uni-konstanz.de
> wrote:
> Dear AMBER users and developers:
>
> It is me again. I searched a little bit more and found PM6 parameters
> for Ca in the qm2_parameters.F90 file. Now it works. Please excuse me
> for not searching there before. Anyway, the two other questions still
> remain:
>
> 1) Are there DFTB parameters for Ca?
> 2) Aqvist or Bradbrook?
>
> Thank you very much again.
> Thomas
>
>
> Thomas Exner wrote:
> > Dear AMBER users and developers:
> >
> > Is there any chance to do QMMM calculations with AMBER if the QM region
> > contains calcium ions? Sander crashes with:
> > QMMM: Atom number: 111 has atomic number 19.
> > QMMM: There are no PM3 parameters for this element. Sorry.
> >
> > I also searched DFTB but there also seem to be no parameters for Ca. Can
> > I add these parameters from a publication like this:
> > Stewart, J.J.P., J Mol Model (2004) 10:155–164
> >
> > And then a somewhat related question: What are the better classical
> > force field parameters for calcium - Aqvist JPC 1990,94,8021 or
> > Bradbrook et al. Journal of the Chemical Society-Faraday Transactions
> > 1998,94,1603
> >
> > Thank you very much.
> > Thomas
> >
> >
>
> --
>
> ________________________________________________________________________________
>
> Dr. Thomas E. Exner
> Theoretische Pharmazeutische Chemie & Biophysik
> Lehrstuhl Pharmazeutische Chemie
> Pharmazeutisches Institut
> Eberhard Karls Universität Tübingen
> Auf der Morgenstelle 8 (Haus B)
> 72076 Tübingen
> Germany
>
> Tel.: +49-(0)7071-2976969
> Mobil: +49-(0)171-3807485
> Fax: +49-(0)7071-295637
> E-Mail: Thomas.Exner[at]uni-tuebingen.de
>
> Fachbereich Chemie und Zukunftskolleg
> Universität Konstanz
> 78457 Konstanz
> Germany
>
> Tel.: +49-(0)7531-882015
> Fax: +49-(0)7531-883587
> E-Mail: Thomas.Exner[at]uni-konstanz.de
>
> ________________________________________________________________________________
>
>
> _______________________________________________
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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
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Fri Nov 15 2013 - 09:30:02 PST
