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. Yo

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

Hello again, I also found out that there is problem with atom typing, which is bypassed while converting molecules (as in my previous reply). The nitrogen should be planar (N.pl3 as in mol2) and its' conformation in sdf file which you've provided is sp3. Pozdrawiam, | Best regards, Maciek

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

We've received the input file. Of course there is problem with it, when you pass it through mol2 file, then your fine. Also obabel reports "-nan" scores for original molecule, which is bad. obabel crystal_ligand_flex.sdf -omol2 | obabel -imol2 --conformer --nconf 2 --writeconformers -o smi Above

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

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 -- View this message in context: http://forums.openbabel.org/Gene

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

Sorry, I missed the request for the input file (still can't see it to be honest). Anyway, I have attached the file. obabel -V gives "Open Babel 2.3.2 -- May 7 2014 -- 09:05:30" i.e. the expected compilation date crystal_ligand.sdf

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

The only message I got during the recompilation was: CMake Error at cmake_install.cmake:88 (FILE): file Internal CMake error when trying to open file: /usr/people/douglas/programs/openbabel-2.3.2_witheigen/openbabel-2.3.2/build/install_manifest.txt for writing. make: *** [install] Error 1

Re: [Open Babel] Generating a diverse set of conformers (Douglas Houston)

abel tmp.sdf -osmi C[C@@H](CC)CC(=O)Cl C[C@@H](CC)CC(=O)Cl C[C@@H](CC)CC(=O)Cl 3 molecules converted On 9 May 2014 10:30, Chris Swain wrote: > > > Message: 2 > Date: Wed, 7 May 2014 05:45:46 -0700 (PDT) > From: Douglas Houston > Subject: Re: [Open Babel] Generating a

Re: [Open Babel] Generating a diverse set of conformers (Douglas Houston)

> > Message: 2 > Date: Wed, 7 May 2014 05:45:46 -0700 (PDT) > From: Douglas Houston > Subject: Re: [Open Babel] Generating a diverse set of conformers > To: openbabel-discuss@lists.sourceforge.net > Message-ID: <1399466746210-4657403.p...@n4.nabble.com> > Conten

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 t

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

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: http://forums.openbabel.org/Generating-a-diverse-set-o

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

obconformer when run outputs: Usage: obconformer NSteps GeomSteps -- 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

So I've recompiled obabel with eigen, but the output of obabel -L ops has not changed: 0xout Additional file output addfilenameAppend input filename to title AddInIndexAppend input index to title AddPolarHAdds hydrogen to polar atoms only canonicalCanonicalize the atom order en

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 di

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 : > Continue by running > obabel -L formats > and > obabel -L ops > > Kin

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

You should compile with Eigen. See the docs ( http://open-babel.readthedocs.org/en/latest/Installation/install.html#requirements ). - Noel On 7 May 2014 11:04, Douglas Houston wrote: > itiwks-> /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel -L > ops > 0xout Additional file o

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

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

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

Continue by running obabel -L formats and obabel -L ops Kind regards, Fredrik Skickat från min iPhone > 7 maj 2014 kl. 11:06 skrev Douglas Houston : > > /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel -L > > outputs: > > charges > descriptors > fingerprints > forcefields > forma

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 G

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 : > Anyone have any comment on this? I am observing the same

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

Have you checked whether these formats and operators are available in your build? See the "-L" option. - Noel On 6 May 2014 18:42, Douglas Houston wrote: > This doesn't work either: > > /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel > crystal_ligand.sdf -oconfbareport -xf tmp.

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

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 [-i] [-o] -O [Options] Try -H option for more in

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 Al

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

> obabel input -O output --conformer --nconf 50 --score rmsd > > - I seem to only get one conformer written to the output file. How can you > produce multiple conformers? If you're using the latest SVN / Git "master" development code, you want; --writeconformers > - Also, it would be great to s

[Open Babel] Generating a diverse set of conformers

This topic has been touched on in other posts but I can't find any explanation about producing multiple conformers with a particular diversity. For example: obabel input -O output --conformer --nconf 50 --score rmsd - I seem to only get one conformer written to the output file. How can you prod