[Open Babel] Generating all cis-trans stereoisomers

Hi, I am trying to generate all cis-trans stereoisomers from a molecule that initially contains no stereo data. Currently, this is my code: For the example molecule (as specified by the SMILES string), the code yields 4 molecules, but two of them are identical. I also tried using [1, 2, 3] in

Re: [Open Babel] GAFF2 in babel?

Is there documentation beyond the Amber source code? Do you know if the difference is just using gaff2.dat instead of gaff.dat? On Wed, Jul 13, 2016 at 4:58 PM, Albert wrote: > Hello: > > I noticed that GAFF2 is released in recent Amber 16. I am just wondering > how can

Re: [Open Babel] GAFF2 in babel?

poking around, it appears there are some new atom types in dat/antechamber/ATOMTYPE_GFF2.DEF . Since AmberTools is GPLv3, I'll leave it to others to decide what that means for the ability to implement gaff2 . I'll note that gaff2.dat is public domain though, so that part should be clean. On Thu,

[Open Babel] obconformer

Hello Guys just got a second question. Thought maybe you can answer them both together If I use obconformer to generate a new conformation of my Ligand: obconformer 250 100 1> 2> log.txt it shows me that the best of the 250 randomly generatet conformation has an energy at somewhere

[Open Babel] obminimize

Hello Guys Currently I'm writing my Bachelorthesis and therefor I'm using Openbabel for some calculations. Now i have the following problems. If i use: obminimize [-ff forcield] [-algorithm] to calculate the minimized energy of a given ligand a don't always get the same results. (of

[Open Babel] GAFF2 in babel?

Hello: I noticed that GAFF2 is released in recent Amber 16. I am just wondering how can we implement it to openBabel? Than you very much Albert -- What NetFlow Analyzer can do for you? Monitors network bandwidth and

[Open Babel] Obconformer / Obminimize

Hello All Now i have the following problem using obminimize. If i use: obminimize [-ff forcield] [-algorithm] to calculate the minimized energy of a given ligand a don't always get the same results. (of course I only compare results of the same ligande, calculated by the same forcefield and