Re: [AMBER] Arsenic force field parametrization

From: Pengfei Li <ambermailpengfei.gmail.com>
Date: Fri, 26 Jun 2015 15:36:18 -0400

Hi Shushi,

I have pre-released a new version (v1.0 Beta2) of pyMSMT. It supports
modeling by using GAMESS-US. You can check this webpage for details:

https://github.com/pengfeili1/pymsmt/wiki

If you have questions, pleas email me.

Best,
Pengfei

2015-06-03 2:17 GMT-04:00 Sushi Shilpa <sushishilpa.gmail.com>:

> Hi Pengfei,
>
>
> Thank you so much for your suggestions, I will with GAMESS.
>
>
>
> Regards
>
> Shilpa T
>
> On Tue, Jun 2, 2015 at 4:26 AM, Pengfei Li <ambermailpengfei.gmail.com>
> wrote:
>
> > Hi Sushi,
> >
> > As Jason suggested. I checked the GAMESS-US and found it could calculate
> > the Hessian matrix and perform ESP charge calculations. I am wondering
> > whether you can get the code? It is free online, here is the web address:
> > http://www.msg.ameslab.gov/gamess/download.html.
> >
> > Best,
> > Pengfei
> >
> > 2015-05-29 15:31 GMT-04:00 Pengfei Li <ambermailpengfei.gmail.com>:
> >
> > > Hi Jason,
> > >
> > > Thanks for your advice. I will check them later.
> > >
> > > All the best,
> > > Pengfei
> > >
> > >
> > > 2015-05-27 11:47 GMT-04:00 Jason Swails <jason.swails.gmail.com>:
> > >
> > >> On Wed, May 27, 2015 at 11:28 AM, Pengfei Li <
> > ambermailpengfei.gmail.com>
> > >> wrote:
> > >>
> > >> > Hi Shilpa,
> > >> >
> > >> > I checked the ORCA program and found that it could generate Hessian
> > >> matrix
> > >> > very easily, which can be used for the force constant calculation.
> But
> > >> it
> > >> > could not perform Merz-Kollman charge calculation. There is a
> > >> replacement
> > >> > for that which is called CHELPG charge calculation, but it is not
> easy
> > >> to
> > >> > generate the charge points on the surface of molecule for the
> > procedures
> > >> > are complicated, while these points are needed for the RESP charge
> > >> fitting.
> > >> > So up to now ORCA can not be a totally replacement for Gaussian. I
> > will
> > >> > still try to find free-charge replacement in the future.
> > >> >
> > >>
> > >> R
> > >> ‚Äč.E.D. tools supports GAMESS, Firefly, and Gaussian (the former two
> are
> > >> released free-of-charge, I think, though they are not open source
> > AFAIK).
> > >>
> > >> So those might be options.
> > >>
> > >> All the best,
> > >> Jason
> > >>
> > >> --
> > >> Jason M. Swails
> > >> BioMaPS,
> > >> Rutgers University
> > >> Postdoctoral Researcher
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> > >
> > > --
> > > Pengfei Li
> > > Ph.D. Candidate
> > > Merz Research Group
> > > Department of Chemistry
> > > Michigan State University
> > >
> >
> >
> >
> > --
> > Pengfei Li
> > Ph.D. Candidate
> > Merz Research Group
> > Department of Chemistry
> > Michigan State University
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>



-- 
Pengfei Li
Ph.D. Candidate
Merz Research Group
Department of Chemistry
Michigan State University
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Received on Fri Jun 26 2015 - 13:00:02 PDT
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