On Thu, Jun 26, 2014 at 4:08 PM, Yingjie Wang <wang1710.umn.edu> wrote:
> Jason,
>
> Thank you very much for your help, especially the script. If I understood
> correctly, there are no existing values of partial charge on butane that
> are directly applicable to the dihedral scan.
Correct. GAFF does not contain a set of charges, it only contains bonded
and Lennard-Jones parameters.
> I need to do RESP fitting
> over a set of conformations to derive the charges. Is that correct?
>
That is the most rigorous approach. The "standard" GAFF approach is to
use am1-bcc charges. The references for this charge model are found in the
Amber manual:
[285] Jakalian, A.; Bush, B.L.; Jack, D.B.; Bayly, C.I. Fast, efficient
generation of high-quality atomic charges.
AM1-BCC model: I. Method. J. Comput. Chem., 2000, 21, 132–146.
[286] Jakalian, A.; Jack, D.B.; Bayly, C.I. Fast, efficient generation of
high-quality atomic charges. AM1-BCC
model: II. Parameterization and Validation. J. Comput. Chem., 2002, 23,
1623–1641.
You can of course also do multi-conformational RESP fitting using the MEP
derived from Gaussian (the R.E.D. tools can help with this;
http://q4md-forcefieldtools.org/
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jun 26 2014 - 15:30:03 PDT
