Center of Excellence Severo Ochoa (2017-2021)
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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:
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> 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
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Nov 29 2018 - 01:00:02 PST
