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
Received on Mon May 11 2020 - 07:30:02 PDT
