[Open Babel] Generating same conformers

Hello, I'm using obabel random conformation generator. I ask for 30 conformers on a system with 30 rotatable dihedrals. Of the 30 conformers, I will only get 10 conformers that are actually different, meaning that I get 3 of the same conformations for each conformer. I would think that asking for

Re: [Open Babel] Remove redundant conformers

Not directly, I'm afraid. The code is in there - this exact functionality is used by Confab and so it should not be too hard to expose, but it's not available at the moment. Do you want to file a feature request at the issue tracker (https://github.com/openbabel/openbabel/issues)? In its absence,

Re: [Open Babel] Generating same conformers

It would be helpful to see the molecule. Certainly, I’d expect that you’d get more variety, but it’s possible you have some symmetric rotors that are not being picked up. -Geoff > On Nov 15, 2017, at 7:50 AM, MD Simulation > wrote: > > Hello, > > I'm using obabel random conformation generat

Re: [Open Babel] Generating same conformers

> Thanks for the reply. I've attached the structure, generated conformers and > a plot of the RMSD from structure 1. Looking at the plot, you get an > oscillatory behavior with the same "random" conformer being generated every > 12 structures. What OS are you using? My guess is that you have

[Open Babel] Filter on error(level)

Hi All, Within obabel there is an option to continue after an error (-e). This function leaves the erroneous entry in the output file. Now I'm looking for an option to filter these erroneous entry from the output. So I would like an option "skip and continue" Is there such an option or is th

Re: [Open Babel] Generating same conformers

I'm running Windows 7 and Open Babel 2.4.1 -- Oct 10 2016 -- 21:27:47 Does obabel sample dihedral angles from the input file, or does it sample from the new dihedral angles? On Wed, Nov 15, 2017 at 11:42 AM, Geoffrey Hutchison < geoff.hutchi...@gmail.com> wrote: > > Thanks for the reply. I've

Re: [Open Babel] [EXTERNAL] Re: Problem Converting .cdx files using Pybel

Hi Stan, Based on your conversation with Pascal, it sounds like a confirmed bug - are you happy to file it in our issue tracker ( https://github.com/openbabel/openbabel/issues)? I can do it with the info you've provided, but it works better if you do it, as you will get updates when someone fixes

Re: [Open Babel] Generating same conformers

> Does obabel sample dihedral angles from the input file, or does it sample > from the new dihedral angles? It samples from the initial geometry. What do you mean by "new dihedral angles?" The presumption of most conformer generation tools is that the set of rotatable bonds is fixed. -Geoff -

Re: [Open Babel] Generating same conformers

You can either take the original structure and rotate a random dihedral by a random angle and continue, always using the original input for the random dihedral rotation or you can use the previously randomized structure for the input to the next random dihedral rotation. The first option will not

Re: [Open Babel] [EXTERNAL] Re: Problem Converting .cdx files using Pybel

> I have attached a new ChemDraw file with some generic structures in it. This > raises the same error I have seen with the other files. I have also included > a screenshot of the OpenBabel GUI conversion of the same .cdx file. I have seen this before (e.g., inside of Avogadro or other progra

[Open Babel] how to save the printed errors in a file

Hi, How can I save/redirect the printed errors in/to a file in obabel? Following did not work obabel *.smi -O *.sdf > out.log Thanks, Jubilant -- Check out the vibrant tech community on one of the world's most engaging t