Carlos -- I'm willing to help with this. Like everyone else, my bandwidth
is pretty limited, but I'll help lift a few things into place (or manage
the lifting of a few things if that is more helpful).
Cheers,
Brent
On Mon, May 11, 2020 at 10:11 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> Tom and I had planned to work on this, but since the pandemic I have not
> had the bandwidth to look into it. If anyone else wants to help out then
> that would be great
> carlos
>
>
> On Wed, May 6, 2020 at 9:17 AM Gustavo Seabra <gustavo.seabra.gmail.com>
> wrote:
>
> > 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.
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > > --
> > > _______________________________________________
> > > 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
_______________________________________________
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 Mon May 11 2020 - 21:00:01 PDT
