Re: [AMBER-Developers] [AMBER] FRCMOD FILE DATABASE

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Wed, 6 May 2020 09:16:39 -0400

Hi everyone,

Question such as this do pop up every once in a while. Would it be
interesting to create an "official" database, where we could keep parameter
files generated for AMBER? initially, I think of some Github or Wiki, but
the most important is that it is linked directly from the Amber website to
make it "authoritative" and easy to find, and maybe maintained (curated?)
by the developers.

What is your opinion?

--
Gustavo Seabra.
On Wed, May 6, 2020 at 8:17 AM Brent Krueger <kruegerb.hope.edu> wrote:
> This probably goes without saying, but there are frcmods for a number of
> molecules (e.g. lipids, GFP-type chromophores, urea) represented in the
> amber tree itself (e.g. amber/dat/leap/parm).
>
>
>
> On Wed, May 6, 2020 at 1:43 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> > I don't really think that this is what you are looking for though I have
> > found it useful for some structures in the past:
> >
> > http://research.bmh.manchester.ac.uk/bryce/amber
> >
> >
> > I have never personally used it though it seems to pop up in conversation
> > from time to time
> >
> > https://upjv.q4md-forcefieldtools.org/RED/
> >
> >
> > Best regards
> >
> > // Gustaf
> >
> > ________________________________
> > Från: Jenny 148 <jenny.rs140.gmail.com>
> > Skickat: den 6 maj 2020 07:33:20
> > Till: AMBER Mailing List
> > Ämne: [AMBER] FRCMOD FILE DATABASE
> >
> > Dear all,
> > Do we have any database which has the prepi and frcmod files of reported
> > structures? I am in need of verifying a few structure parameters and need
> > some reference. I have a series of aromatic rings- like quinolinium ring
> ,
> > indole ring and so on. Please syggest if there is some webserver which
> has
> > ligand parameters.
> >
> > Thank you.
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> >
>
>
> --
> _______________________________________________
> Brent P. Krueger  (he/him/his)......phone:   616 395 7629
> Professor......................................fax:       616 395 7118
> Hope College...............................Schaap Hall 2120
> Department of Chemistry
> Holland, MI     49423
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Received on Wed May 06 2020 - 06:30:06 PDT