Re: [AMBER] Partial Charges in AMBE force field

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Sun, 18 Aug 2013 17:29:35 +0200

Dear BERGY,

> I which to know the changes in partial charges over the years in amber
> force field from parm94 tol ff12SB.
> and the QM methods that was used to calculate the partial charges.
> Can anyone suggest me the reference for the same.

Amber force fields use RESP charges. For the additive model see:
http://ambermd.org/doc6/html/AMBER-sh-19.4.html#sh-19.4
http://pubs.acs.org/doi/abs/10.1021/ja00074a030
http://pubs.acs.org/doi/abs/10.1021/j100142a004
http://onlinelibrary.wiley.com/doi/10.1002/jcc.540161106/abstract
http://doi.wiley.com/10.1002/jcc.10349
  &
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/

> I have calculated partial charges for bases and find it different from the
> one in amber ff12sb.

MEP based charges are not reproducible - this was discussed many times
in the past in the Amber mailing list. If you want to derive
reproducible charge values better using R.E.D. at
http://q4md-forcefieldtools.org/RED/ and the RBRA approach; see
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/.

R.E.D. Server at http://q4md-forcefieldtools.org/REDS/ is also
available and it provides all (hardware & software) what is required
for MEP based charge derivation and force field library building.

regards, Francois



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Received on Sun Aug 18 2013 - 09:00:02 PDT