Re: [Open Babel] Generating a diverse set of conformers

Can I just check people received the input file? I used the Nabble forum to attach it ... -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657429.html Sent from the General discussion mailing list archive at Nabble.com.

Re: [Open Babel] Generating a diverse set of conformers

I wrote this reply yesterday, but it didn’t make it to the babble list somehow. When I try obabel ~/Desktop/crystal_ligand_flex.sdf -O tst-res.sdf --confab --conf 5 (with your example file), I get a file with 2900 conformers written, so I believe there is a problem with your installation.

Re: [Open Babel] Generating a diverse set of conformers

Actually that input file isn't the most flexible, here is a different one that is more flexible and also only generates one conformer. crystal_ligand_flex.sdf http://forums.openbabel.org/file/n4657427/crystal_ligand_flex.sdf -- View this message in context:

Re: [Open Babel] Generating a diverse set of conformers

It's gone worryingly quiet ... -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657420.html Sent from the General discussion mailing list archive at Nabble.com.

Re: [Open Babel] Generating a diverse set of conformers

Well, you have been asked to provide your input file for easier debugging, one option could be to try that… Anyway, obconformer only outputs one conformer according to it’s documentation, that one is written on stdout, so it’s included in your output (which by the way didn’t appear when I read

Re: [Open Babel] Generating a diverse set of conformers

Hi, Does the input file contain 3D-coordinates? As far as I have seen, neither confab nor conformer will generate an initial 3D structure if it’s not already present. Kind regards, Fredrik 6 maj 2014 kl. 19:39 skrev Douglas Houston dhous...@staffmail.ed.ac.uk: Anyone have any comment on

Re: [Open Babel] Generating a diverse set of conformers

/usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel -L outputs: charges descriptors fingerprints forcefields formats loaders ops How do I tell? -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657397.html Sent from the

Re: [Open Babel] Generating a diverse set of conformers

itiwks- /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel -L ops 0xoutfile.xxx Additional file output addfilenameAppend input filename to title AddInIndexAppend input index to title AddPolarHAdds hydrogen to polar atoms only canonicalCanonicalize the atom order

Re: [Open Babel] Generating a diverse set of conformers

Hi, Is the input molecule flexible? It would be much easier to test if you could sent it to the list. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2014-05-07 11:19 GMT+02:00 Fredrik Wallner fred...@wallner.nu: Continue by running obabel -L formats and obabel

Re: [Open Babel] Generating a diverse set of conformers

OK will do. Just out of curiosity, what is my install of Babel doing when I specify those options? Just ignoring them, without informing the user? -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657402.html Sent from the General

Re: [Open Babel] Generating a diverse set of conformers

obconformer when run outputs: Usage: obconformer NSteps GeomSteps file -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657404.html Sent from the General discussion mailing list archive at Nabble.com.

Re: [Open Babel] Generating a diverse set of conformers

obconformer with arguments: /usr/local/bin/obconformer 10 10 crystal_ligand.sdf outputs: The conformers appear to be generated - how do I get them written out? The input structure is in 3D by the way. -- View this message in context:

Re: [Open Babel] Generating a diverse set of conformers

This doesn't work either: /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel crystal_ligand.sdf -oconfbareport -xf tmp.sdf -xr 1.0 I get: obabel: cannot write output format! Open Babel 2.3.2 -- Mar 20 2013 -- 08:59:03 Usage: obabel [-iinput-type] infilename [-ooutput-type]

Re: [Open Babel] Generating a diverse set of conformers

Anyone have any comment on this? I am observing the same problem as OP. I am using the following: /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel crystal_ligand.sdf -O tmp.sdf --conformer --nconf 50 --writeconformers I only get 1 conformer in the 1 output file. I have also tried

Re: [Open Babel] Generating a diverse set of conformers

Thanks for the comments. I am using Open Babel 2.3.1 on a mac. The command still doesn't ouptut multiple conformers, only the one file with one conformer in it. obabel input.sdf -O out.sdf --conformer --nconf 50 --score rmsd obabel input.sdf -O out.sdf --writeconformers --nconf 50 --score rmsd