VMD-L Mailing List

From: Paweł Kędzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Wed Sep 22 2021 - 04:56:10 CDT

W dniu 22.09.2021 o 10:02, Daniel Fellner pisze:
> Hi everyone,
>
> I was wondering if there was a simple way to generate multiple
> Gaussian input files for conformers of a molecule originating from one
> mol2 (or pdb) file? There are too many conformers to do it manually
> editing the First and Last fields in Save Coordinates.

It is probably possible in VMD with some scripting, but the quickest
solution which came to my mind is to use Open Babel
<https://urldefense.com/v3/__https://openbabel.org/wiki/Main_Page__;!!DZ3fjg!t1-izUyJPhU8sFNW65xM3iK0fHZ6bwK56ue0KCYCTSKTFAtBCSTrbDzl2VKm5fyPqw$ > command line:

obabel -imol2 input.mol2 -ogau -O output.gau -xk "#B3LYP/6-31+G** OPT FREQ" -m

After option -xk you can specify whatever you want in the Gaussian route
line, -m splits the molecules from the input into separate files
output1.gau, output2.gau etc.

Open Babel can actually do much more, like add missing hydrogens,
generate 3D coordinates from 2D, SMILES or InChl codes, or even generate
the conformers for you:

https://urldefense.com/v3/__https://open-babel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html__;!!DZ3fjg!t1-izUyJPhU8sFNW65xM3iK0fHZ6bwK56ue0KCYCTSKTFAtBCSTrbDzl2VLRvA4s7A$

HTH,

Pawel

>
> *Daniel Fellner BSc(Hons)*
> PhD Candidate
> School of Chemical Sciences
> University of Auckland
> Ph +64211605326