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
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >>
> >> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo
> >> /amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!O17LEeXQ1OBXwzTktJhx4KPTeYr_tNx
> >> 1yFOLRLOc5cdl2zCjZKuSgxK1Mn6bAUVS0-pDwyHUuc7TsA$
> >>
> >
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Received on Sat Oct 29 2022 - 14:00:03 PDT
