[Open Babel] Confab not generating structures

Hello, I'm using the most recent version of OpenBabel (2.4.1) on Windows. I am having trouble getting Confab to generate structures based on the attached structure. I am using the command: >>> obabel polymer.mol2 -O confs.mol2 --confab --conf 1 --verbose This is the output: ""

[Open Babel] Get molecular descriptor

Hello, I see that obabel has a number of built-in descriptors (obabel -L descriptors). Is it possible to pass in a structure file and get the descriptor information? For example, I have conf.xyz and I would like the number of bonds, is it possible to do something like: obabel conf.xyz --descrip

[Open Babel] Remove similar conformers

Hello, Is it possible to pass in a list of 3D conformers (xyz, mol2,...) and remove structures that are within a specified RMSD? Thanks! -- Check out the vibrant tech community on one of the world's most engaging tech sit

[Open Babel] OBProp calculated descriptors

Hi, Could someone point me in the right direction of where OBProp is calculating some of the descriptors? I'm mainly interested in how it's getting values for logP, PSA and MR. Thanks! -- Check out the vibrant tech commu

[Open Babel] Remove redundant conformers

Hello, I have about 100 conformers. Some of those are similar based on RMSD when looked at in VMD. I would like to eliminate redundant conformers based on RMSD. Is there a way to do that within Open Babel? Thanks Carrie --

[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] 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] 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

[Open Babel] Avogadro - Al2O3 0001 Surface

Hello, This may be the wrong mailing list so I apologize in advance. Is it possible to build the aluminum oxide 0001 surface in Avogadro? Thanks, Stacey ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforg

[Open Babel] Openbabel and Python 3.8

Hello, I followed the instructions to install Openbabel using pip from: https://open-babel.readthedocs.io/en/latest/UseTheLibrary/PythonInstall.html#windows I'm using Python 3.8 and have installed the most recent Openbabl but when I tried to use pip, the installation of the python bindings fai

Re: [Open Babel] Openbabel and Python 3.8

What Python version is supported? Thanks! On Tue, May 26, 2020, 3:39 AM Noel O'Boyle wrote: > 3.8 is not supported on Windows. > > On Mon, 25 May 2020, 19:54 MD Simulation, > wrote: > >> Hello, >> >> I followed the instructions to install Openbabel

[Open Babel] obabel genetic does not sample amide bonds

Hello, I am trying to generate conformers of a structure with two amide bonds but the genetic method does not sample the amide bonds. Is there a way to sample those bonds? Thanks, Stacey ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.source

[Open Babel] indexing atoms in png file

Hello, I see in an svg file, I can index the elements with "-xi", but I don't see this option with a png file. Is it possible? Thanks, Frank ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/