[Open Babel] Fwd: Error in file conversion

Dear all, I see that when I convert the attached file from sdf to pdb or pdbqt, Obabel guesses a few atoms as ALA (could be an amino acid Alanine) and changes its atom name to ALA. Does anyone know any possible cause and how to avoid this? I am posting this again as I didn't get an answer for this

[Open Babel] Error in file conversion

Dear all, I see that when I convert a file from sdf to pdb or pdbqt. Obabel guesses a few atoms as ALA (could be an amino acid Alanine). Does anyone know any possible cause? Attached are the files. Thanks, Jubilant 443884.sdf Description: Binary data 443884.pdb Description: Protein Databank

[Open Babel] netcharge of a molecule

Hi everyone, How to calculate the net charge of a molecule in openbabel? Thanks, Jubilant -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot_

Re: [Open Babel] Best way to convert pdbqt to pdb

Here are the files. I see that when I convert the file from sdf to pdb or pdbqt. Obabel guesses a few atoms as ALA (could be an amino acid Alanine). Do you know any possible cause? Thanks, Jubilant On Wed, Jan 24, 2018 at 10:51 AM, Geoffrey Hutchison < geoff.hutchi...@gmail.com> wrote: > > I us

[Open Babel] Best way to convert pdbqt to pdb

Hi everyone, What is the best way to convert pdbqt to pdb? I used openbabel to do this. It worked mostly fine but with a few compounds, specially with the ones have protonated Nitrogen, gets destroyed. Thanks, Jubilant --

Re: [Open Babel] Aromaticity

e of thumb here? Do you recommend any means to check the correctness of aromaticity after the conversion? Thanks, Sundar On Mon, Dec 4, 2017 at 7:18 AM, Noel O'Boyle wrote: > HI Jubilant, > > The development version has rewritten handling of aromaticity, and as this > will be t

[Open Babel] Obabel warning while pdb to sdf conversion

Hi Openbabel users, I have a following warnings while trying to convert a set pdbs to sdf or smi. Can someone give an insight on it? obabel pdb/*.pdb -O test.sdf == *** Open Babel Warning in parseAtomRecord WARNING: Problems reading a PDB file Problems reading a H

[Open Babel] Aromaticity

Hi all, I was looking for a documentation for how openbabel works on detecting aromaticity and what is the flag to choose while converting molecules. Does obabel detect and fix aromaticity by default? If yes, what are the default options and what other options are available? Please, direct me to

[Open Babel] how to save the printed errors in a file

Hi, How can I save/redirect the printed errors in/to a file in obabel? Following did not work obabel *.smi -O *.sdf > out.log Thanks, Jubilant -- Check out the vibrant tech community on one of the world's most engaging t

Re: [Open Babel] extract a single compound from a multimolecular sdf

Hi David, 9782 is not the 9782th molecule in the file. I also will have to loop through sdf for various other numbers. I asked this as an example. Thanks, Sundar On Sun, Nov 5, 2017 at 7:13 PM, David Hall wrote: > Assuming you want the 9782’th molecule in the file, using the -f and

[Open Babel] extract a single compound from a multimolecular sdf

Hi, I was trying to extract a single molecule from a multimolecular sdf. I used the following but it didn't work. obabel ../input/in-3D.sdf -O 9782.sdf --filter "title='9782'" Let me how can I do this. Thanks, Jubilant

Re: [Open Babel] gen3d doesn't convert all compounds

Hi David and Geoff, I ran the calculation again to reproduce the problem and realized that it was my computer's memory that caused the program to abort not converting all the compounds. This time it converted all compounds. So no worries there. I still got several following warnings though. "*** O

Re: [Open Babel] single sdf to multi pdbs conversion with compound names

Hi Chris, Worked like a charm. Thanks a lot. But I couldn't find a documentation for --split All I see is --splitinto docs. -Jubilant On Wed, Oct 25, 2017 at 4:08 AM, Chris Morley wrote: > On 25/10/2017 07:55, Sundar wrote: > > Can anyone help me convert a single input (multi

[Open Babel] single sdf to multi pdbs conversion with compound names

Hi, Can anyone help me convert a single input (multimolecular) sdf file into multiple pdb files with the molecule names (as seen in the sdf file) as their file names instead of consecutively numbered file names? Thanks, Jubilant

Re: [Open Babel] obminimize outputs only in pdb (multimolecule pdb)

step i.e. converting multimolecular pdb to sdf? Thanks, Sundar On Thu, Oct 19, 2017 at 8:01 PM, Sundar Jubilant wrote: > Thanks. I will try that. > > Sundar Thangapandian > > > On Oct 19, 2017, at 6:40 PM, Geoffrey Hutchison < > geoff.hutchi...@gmail.com> wrote: >

Re: [Open Babel] obminimize outputs only in pdb (multimolecule pdb)

Thanks. I will try that. Sundar Thangapandian > On Oct 19, 2017, at 6:40 PM, Geoffrey Hutchison > wrote: > > The obminimize program does not have all the features of the obabel command. > You can naturally convert a PDB file to SDF: > > obabel file.pdb -O file.sd

Re: [Open Babel] building openbabel with no root access

I found the respective section and it worked all well. Thanks Jubilant > On Oct 16, 2017, at 2:02 PM, Dimitri Maziuk wrote: > >> On 10/16/2017 01:50 PM, Noel O'Boyle wrote: >> Have you read the section in the docs that describes how to do that? > > I suspect the issue that if gcc and all req

[Open Babel] building openbabel with no root access

Hi, I would like to build openbabel in a local folder on a linux machine. I don't have root access to this machine. Help me out with it. -Jubilant -- Check out the vibrant tech community on one of the world's most engagin

Re: [Open Babel] gen3d doesn't convert all compounds

Yes. Sundar Thangapandian > On Oct 13, 2017, at 3:08 PM, David Hall wrote: > > I assume your second command is actually using output2D.sdf as input? > > -David > >> On Oct 13, 2017, at 3:46 PM, Sundar wrote: >> >> Sure. >> Here it goes. >>

Re: [Open Babel] gen3d doesn't convert all compounds

Sure. Here it goes. obabel input.smi -h -r -b -c --unique --gen2d --partialcharge mmff94 -O output2D.sdf obabel output3D.sdf --gen3d -O output3D.sdf output2D.sdf contains 7581 compounds exactly as in input.smi but output3D.sdf only has 881 compounds. Thanks, Sundar On Fri, Oct 13, 2017 at 2

[Open Babel] obminimize outputs only in pdb (multimolecule pdb)

Hi, obminimize outputs only in pdb format. I tried -osdf filename.sdf and it didn't work. How can I get it in sdf format? Or how can I convert multimolecule pdb file to an sdf file? Thanks, Sundar -- Check ou

Re: [Open Babel] gen3d doesn't convert all compounds

duplicates. My guess is that you have only > 800 unique compounds. > > Regards, > - Noel > > On 13 October 2017 at 11:58, Sundar wrote: > >> Hi everyone, >> >> I am pretty new to OB. I am trying to convert a database of compounds >> (~7000) from smile

[Open Babel] gen3d doesn't convert all compounds

Hi everyone, I am pretty new to OB. I am trying to convert a database of compounds (~7000) from smiles to 3D. I first converted them into 2D using -h -r --unique -b -c --partialcharge mmff94 followed by --gen3d. It only converted ~800 compounds saying nothing about other conformers. Any idea it be