Re: [AMBER] Antechamber with QM software other than Gaussian

From: Alexander Izvorski via AMBER <amber.ambermd.org>
Date: Sat, 29 Oct 2022 14:41:31 -0700

Hi Barış - Thanks! There are actually quite a lot of re-implementations of
RESP outside of Antechamber. I'd like to use Antechamber if at all
possible, for consistency: ideally just swap out the QM software, but keep
the code doing the fit and the options used for the fit exactly the same.
I think that's probably something quite a lot of folks want, especially if
they're not working on new fitting algorithms but just want to use the most
standard way to do a fit.

All that is necessary for that is to write some code to generate the
points, and then some code to reformat the potential values into a
GAMESS-like format to feed into Antechamber. Do you happen to know of code
that generates the points?

Best,
Alex


On Sat, Oct 29, 2022 at 1:49 PM Barış KURT via AMBER <amber.ambermd.org>
wrote:

> with this python implementation, you can calculate resp charges:
> https://github.com/cdsgroup/resp (please cite the references in the page)
>
>
> James Kress via AMBER <amber.ambermd.org>, 29 Eki 2022 Cmt, 23:38
> tarihinde
> şunu yazdı:
>
> > Have you tried generating a ESP cube and using that? It gives you ESP
> in a
> > 3D collection of points surrounding the molecule.
> >
> > -----Original Message-----
> > From: Alexander Izvorski via AMBER <amber.ambermd.org>
> > Sent: Saturday, October 29, 2022 4:07 PM
> > To: Shiji Zhao <shijiz.uci.edu>
> > Cc: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] Antechamber with QM software other than Gaussian
> >
> > Hi Shiji,
> >
> > Yes, it seems like antechamber does accept GAMESS outputs, using the -fi
> > gamess option. This option is mostly undocumented, antechamber -L lists
> it
> > but the Amber manual does not.
> >
> > The complete command is something like this:
> >
> > antechamber -i test.dat -fi gamess -o resp.mol2 -fo mol2 -c resp -eq 2
> >
> > The same input works in espgen -i test.dat -o test.esp (the format is
> > apparently autodetected). I've tested with ambertools=22.0 and 20.9.
> >
> > Here test.dat is what GAMESS calls a "punch" file. I have some examples
> of
> > the file format, please let me know if you'd like to have a look. GAMESS
> > generates its own points at which to evaluate the potential, these seem
> > very
> > similar to Gaussian.
> >
> > I am happy I got this working, but would still really like to be able to
> do
> > the same thing for other QM software, especially the software already
> > bundled with Amber, and software which can be installed directly from
> > conda-forge :)
> >
> > The tricky part is generating the points - Orca, Psi4, etc can easily
> > calculate potential-at-a-point, but don't have any builtin function to
> find
> > the points on Connoly-type surfaces around the provided atoms. Do you
> have
> > any example code which calculates the coordinates of the points?
> >
> > Best,
> > Alex
> >
> >
> >
> >
> >
> > On Tue, Oct 18, 2022 at 12:34 AM Shiji Zhao <shijiz.uci.edu> wrote:
> >
> > > Hi Alexander,
> > >
> > > I read the source code of espgen.c in AmberTools and noticed it has
> > > added support to GAMESS. The espgen version is 1.1.
> > >
> > > I have never used GAMESS before. Maybe you can give it a try and let
> > > me know if espgen can handle GAMESS output files. This information
> > > will also be helpful to me since I am considering adding more features
> > > to the espgen code.
> > >
> > > Best,
> > > Shiji
> > >
> > > On Thu, Jul 7, 2022 at 5:58 PM Alexander Izvorski via AMBER <
> > > amber.ambermd.org> wrote:
> > >
> > >> Hello Amber folks,
> > >>
> > >> I'd like to use antechamber and espgen/respgen to fit RESP charges
> > >> without using Gaussian.
> > >>
> > >> I'd be potentially interested in any other QM software: QUICK (which
> > >> is nice because it's now bundled with ambertools), Psi4, CP2K,
> > >> GAMESS, Orca etc. It just seems a bit limiting to have Gaussian be
> > >> the only choice for this type of calculation.
> > >>
> > >> The latest Amber22 manual seems to assume Gaussian-only in a few
> places:
> > >>
> > >> 15.3.5. espgen
> > >> > Espgen reads in a gaussian (92,94,98,03) output file and extracts
> > >> > the
> > >> ESP
> > >> > information
> > >> >
> > >> > 15.1.1. antechamber
> > >> > -ge gaussian esp file generated by iop(6/50=1), default is g09.gesp
> > >> >
> > >>
> > >> Has anyone successfully used non-Gaussian software for RESP? Are
> > >> there any supported options?
> > >>
> > >> If not, could someone describe the expected output file format from
> > >> Gaussian? I can probably try to write a format converter, since most
> > >> of the tools mentioned above can calculate and save electrostatic
> > potential.
> > >> For example Psi4 has the GRID_ESP
> > >> <
> > >> https://urldefense.com/v3/__https://psicode.org/psi4manual/master/oep
> > >> rop.html__;!!CzAuKJ42GuquVTTmVmPViYEvSg!O17LEeXQ1OBXwzTktJhx4KPTeYr_t
> > >> Nx1yFOLRLOc5cdl2zCjZKuSgxK1Mn6bAUVS0-pDwyFA1PkLTw$
> > >> > option. I just don't
> > >> have any idea what the espgen or respgen-compatible format should
> > >> look like.
> > >>
> > >> Best,
> > >> Alex
> > >> _______________________________________________
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> > >> AMBER.ambermd.org
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> > >> 1yFOLRLOc5cdl2zCjZKuSgxK1Mn6bAUVS0-pDwyHUuc7TsA$
> > >>
> > >
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Received on Sat Oct 29 2022 - 15:00:02 PDT
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