Re: [Open Babel] error compiling openbabel

You didn't say what version of OB or Ubuntu. Try the latest OB dev version, and let us know if it doesn't work. - Noel On 16 November 2015 at 16:15, Osvaldo Martin wrote: > I am trying to compile openbabel on Ubuntu (to make it work with python3) > and I when I execute

Re: [Open Babel] Problem in converting a PDB file to MOL2

On 11/19/2015 10:17 AM, Dimitri Maziuk wrote: > I think our best option --^^^ That was supposed to be "your" -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature

Re: [Open Babel] Problem in converting a PDB file to MOL2

On 11/19/2015 05:07 PM, Alexandre Fassio wrote: ... Apparently, they don't have a > ligand defined on the Chemical Component Dictionary that would represent > these assembled ligands. As I understand it, they'll make a separate "compound" ligand for things that they see often, like in drugs -- I

[Open Babel] atom names stripped in OBminimize

Hello I recently noted with the help of a colleague that atom names were not being output properly after an OBminimization operation on a pdb file, especially one that contains a Bromine atom. The command I use is obminimize -ff UFF -sd -n 5000 -opdb ligand.pdb > ligandMin.pdb The input

Re: [Open Babel] Problem in converting a PDB file to MOL2

Pascal Muller-3 wrote > Hi, > > > >> Right, it's true. But, for example, if I have 8 ligands covalently bonded >> I >> would like to consider these 8 ligands as it were only one ligand and >> search >> on the mmCIF dictionary for a ligand that represents the 8 ligands >> together. >> Because by

Re: [Open Babel] Problem in converting a PDB file to MOL2

Dimitri Maziuk wrote > On 2015-11-19 05:28, Alexandre Fassio wrote: > >> Right, it's true. But, for example, if I have 8 ligands covalently bonded >> I >> would like to consider these 8 ligands as it were only one ligand and >> search >> on the mmCIF dictionary for a ligand that represents the 8

Re: [Open Babel] Problem in converting a PDB file to MOL2

Dimitri Maziuk wrote > On 2015-11-18 05:05, Alexandre Fassio wrote: > >> For example, a cellobiose can be represented as two glucoses (GLCs). >> Thus, >> it is difficult to know without a previous knowledge, which ligand is >> represented by these two GLCs. >> >> In another case, I had a PDB with

Re: [Open Babel] Problem in converting a PDB file to MOL2

On 2015-11-19 05:28, Alexandre Fassio wrote: > Right, it's true. But, for example, if I have 8 ligands covalently bonded I > would like to consider these 8 ligands as it were only one ligand and search > on the mmCIF dictionary for a ligand that represents the 8 ligands together. > Because by

Re: [Open Babel] Problem in converting a PDB file to MOL2

Hi, > Right, it's true. But, for example, if I have 8 ligands covalently bonded I > would like to consider these 8 ligands as it were only one ligand and > search > on the mmCIF dictionary for a ligand that represents the 8 ligands > together. > Because by searching an ID for each ligand