Re: [AMBER] Combining GAFF and GLYCAM force fields to describe a non-natural sugar

From: José Daniel Martinez <jmartinez.cicbiogune.es>
Date: Thu, 29 Nov 2018 08:52:44 +0000

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: > 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 _______________________________________________ AMBER mailing list AMBER@ambermd.org http://lists.ambermd.org/mailman/listinfo/amber

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Received on Thu Nov 29 2018 - 01:00:02 PST
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