Re: [Rdkit-discuss] Issues with rdkit and postgresql cartridge conda installation

Hi Larson, On Fri, Oct 14, 2016 at 6:17 PM, Danes, Larson wrote: > > First and foremost, please excuse any inaccuracies as I am new to the world of Cheminformatics. I'll start with some background on my issue. I've got a MySQL database with chemical information such as

[Rdkit-discuss] Solved! (was, Re: Fwd: Jupyter renders only from the outermost level?)

In an earlier thread, I reported that I could not get Jupyter to render except from the outermost level of the notebook. For instance, the following code would not render Benzene: -- from rdkit import Chem from rdkit.Chem import rdDepictor from rdkit.Chem.Draw import rdMolDraw2D from

Re: [Rdkit-discuss] gromacs force field and topology from SMILES

Hi Rafal, as far as I know the MMFF is not compatible with any contemporary MD forcefield. The usual way to generate topologies for ligands is the generalised amber forcefield (GAFF). What you need are ambertools (http://ambermd.org/ ) and acpype

[Rdkit-discuss] windows 32 shared library

Has anyone compiled rdkit into a 32bit shared library dll? Steven Combs -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org!

Re: [Rdkit-discuss] gromacs force field and topology from SMILES

Dear Rafal, answers below. On 10/14/16 13:53, Rafal Roszak wrote: > Dear all, > > 1. I want to generate gromacs topology with force field parameters > from SMILES. RDKit has two FFs so this should be easy task at least for > this two force fields. Bond and angle parameters can be simply take >

[Rdkit-discuss] gromacs force field and topology from SMILES

Dear all, 1. I want to generate gromacs topology with force field parameters from SMILES. RDKit has two FFs so this should be easy task at least for this two force fields. Bond and angle parameters can be simply take from Get*BondStretchParams and Get*StretchBendParams, but vdW and torsian