If you've done force field development / charge fitting with Gaussian and
you know in principle what you're trying to do, I think you'll find mdgx
intuitive and easy to use. The configuration sampling that it can do is a
big win--as long as oyu've got a decent "guess" force field it makes you
any number of structures that sample the conformational space and are
energy minimized with respect to other degrees of freedom. I'm working to
extend its capabilities for the next release cycle.
Dave
On Thu, Nov 29, 2018 at 3:52 AM José Daniel Martinez <
jmartinez.cicbiogune.es> wrote:
> Center of Excellence Severo Ochoa (2017-2021)
>
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> ---------- Forwarded message ----------
> From: "José Daniel Martinez" <jmartinez.cicbiogune.es>
> To: AMBER Mailing List <amber.ambermd.org>
> Cc:
> Bcc:
> Date: Thu, 29 Nov 2018 08:52:44 +0000
> Subject: Re: [AMBER] Combining GAFF and GLYCAM force fields to describe a
> non-natural sugar
> Thanks Lachele,
> I will follow your advice.
>
>
> Dani.
> ________________________________________
> De: Lachele Foley <lf.list.gmail.com>
> Enviado: miércoles, 28 de noviembre de 2018 20:19
> Para: AMBER Mailing List
> Asunto: Re: [AMBER] Combining GAFF and GLYCAM force fields to describe a
> non-natural sugar
>
> You might also consider posting this question to the GLYCAM-L list. The
> folks who develop glycam tend to listen there.
>
> GLYCAM-L mailing list: https://listserv.uga.edu/cgi-bin/wa?A0=GLYCAM-L
>
>
> On Wed, Nov 28, 2018 at 1:54 PM David Cerutti <dscerutti.gmail.com> wrote:
>
> > This email is in no way intended to impede workplace productivity, create
> > environmental hazards, or disseminate political disinformation. If you
> > believe you have received this email in error, please understand it is
> > intended specifically for you. You. The contents of this mail have been
> > checked by the author, but no guarantees are made as to its authenticity
> > and no assurances are given as to the physical well being of any subjects
> > discussed herein. Any grammatical errors are the responsibility of the
> > author, except for instances of purple prose or the passive voice being
> > used which are purely the products of the whimsically delightful
> Grammarly
> > program with extreme settings in Preferences >> Advanced.
> >
> > Center for Force Field Research Excellence, Rutgers University
> > * * * * *
> >
> > The way I'd approach this sugars problem is to take the base parameters
> > from GLYCAM and try to graft in the fluorine chemistry. GAFF isn't the
> > tool here, I think--it is for making something from scratch, whereas you
> > want something that looks like an established parameter set for related
> > molecules. What I'd do is make your residue, assign charges based on
> > GLYCAM manually (use your best judgment), then take the mdgx program in
> > AmberTools. Look at these tutorials:
> >
> > http://ambermd.org/tutorials/advanced/tutorial28/index.php
> > http://ambermd.org/tutorials/advanced/tutorial32/index.php
> >
> > The first one is about "IPolQ" charges which you don't want if you are
> > trying to mimic GLYCAM--you want HF/6-31G* or HF/CC-PVTZ. The thing to
> do
> > is run mdgx -FITQ to see a list of options for charge fitting, then make
> a
> > bunch of configurations and run HF/(your basis set) on them to get charge
> > grids. mdgx will be able to take those charge grids and run a REsP-like
> > fit, and you can specify that it hold charges other than the fluorine and
> > proximal atoms to values from the original GLYCAM for the sugars that
> > you've decided are the closest match. Then, you can make a bunch of
> other
> > configurations by manipulating the fluorine group to sample dihedral
> > configurations, and refit parameters that impinge on the motion of that
> > group (I'd recommend angles as well as dihedrals).
> >
> > This is the "hard core" way to do it, but I made mdgx to make the
> hardcore
> > stuff as straightforward as possible. It's mechanistically easier to
> take
> > mdgx and make a completely new set of parameters for your molecule, but
> > it'll take more computational power and the details of telling mdgx to
> > respect certain parameters from GLYCAM are not that difficult.
> >
> > Dave
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
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Received on Thu Nov 29 2018 - 09:30:02 PST
