From owner-chemistry(+ at +)ccl.net Wed Apr 27 11:46:01 2022 From: "marius bouba ousmanou mariusolaar3(~)gmail.com" To: CCL Subject: CCL:G: Overlaying conformers for visualization Message-Id: <-54650-220427012432-532-+j7chJ6BvDaCdGL6LQKV+w!^!server.ccl.net> X-Original-From: marius bouba ousmanou Content-Type: multipart/alternative; boundary="000000000000de162e05dd9c0508" Date: Wed, 27 Apr 2022 06:24:14 +0100 MIME-Version: 1.0 Sent to CCL by: marius bouba ousmanou [mariusolaar3[-]gmail.com] --000000000000de162e05dd9c0508 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hello everyone Dear Andrew, As contribution, it is better to use gaussView5.0 rather than 6.0 version. So you Can extract the geometry optimization curve. But basically, you Can manually extract molecular coordinates by searching. "Standard orientation" from your log file. Then all the optimized g=C3=A9om=C3=A9tries Can be respectively edited from these g=C3= =A9om=C3=A9tries. Best regards. Marius Bouba Ousmanou Le mer. 27 avr. 2022 =C3=A0 04:02, Andrew DeYoung andrewdaviddeyoung**gmail= .com < owner-chemistry]|[ccl.net> a =C3=A9crit : > Hi, > > I'm a postdoc and quantum chemistry novice. I've run geometry > optimization ("Opt") using Gaussian to find several molecular geometries > corresponding to local minima on the potential energy surface for a singl= e > molecule. The geometries are similar but not exact. I'd like to overlay > several geometries in order to visualize, qualitatively, how they differ. > In other words I want to overlay multiple conformers. > > Could someone please suggest a relatively simple way to overlay geometrie= s > for visualization? I have access to GaussView, Avogadro, VMD, and any > other freeware applications you can think of. The molecular geometries a= re > in separate .log files (i.e., output from Gaussian), but of course it is > easy to convert these to almost any other chemical file format, using > Avogadro or the like. > > I realize, though, that "overlaying several conformers" is not a unique > specification; one would need to specify which atom(s) to try to overlap > exactly. Is there an algorithm in a computational chemistry program that > does this? > > Thank you for any guidance you can provide! > > Andrew > > Andrew DeYoung, PhD > Department of Chemistry > Carnegie Mellon University > --000000000000de162e05dd9c0508 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello everyone
<= br>
Dear Andrew,
As contribution, it is better to use gaussView5.0 rather than 6.0 ver= sion. So you Can extract the geometry optimization curve.=C2=A0
But basically, you Can manually extract molecular=C2=A0 coordin= ates by searching. "Standard orientation" from your log file. The= n all the optimized g=C3=A9om=C3=A9tries Can be respectively edited from th= ese g=C3=A9om=C3=A9tries.=C2=A0

Best regards.
Marius Bouba Ousmanou
<= /div>

Le mer. 27 avr. 2022 =C3=A0 04:02, Andrew DeYoung andrewdaviddeyoung**= gmail.com <owner-chemistry]|[ccl.net> a =C3=A9crit=C2=A0:
Hi,

I&#= 39;m a postdoc and quantum chemistry novice.=C2=A0 I've run geometry op= timization ("Opt") using Gaussian to find several molecular geome= tries corresponding to local minima on the potential energy surface for a s= ingle molecule.=C2=A0 The geometries are similar but not exact.=C2=A0 I'= ;d like to overlay several geometries in order to visualize, qualitatively,= how they differ.=C2=A0 In other words I want to overlay multiple conformer= s.

Could someone please suggest a relatively=C2=A0= simple way to overlay geometries for visualization?=C2=A0 I have access to = GaussView, Avogadro, VMD, and any other freeware applications you can think= of.=C2=A0 The molecular geometries are in separate .log files (i.e., outpu= t from Gaussian), but of course it is easy to convert these to almost any o= ther chemical file format, using Avogadro or the like.

=
I realize, though, that "overlaying several conformers" is n= ot a unique specification; one would need to specify which atom(s) to try t= o overlap exactly.=C2=A0 Is there an algorithm in a computational chemistry= program that does this?

Thank you for any guidanc= e you can provide!

Andrew

Andrew DeYoung, PhD
Department of Chemistry
Carnegie M= ellon University
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