[Open Babel] Fwd: Error in file conversion

[Sundar]

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 before.

Attached are the files.

Thanks,
Jubilant


443884.sdf
Description: Binary data


443884.pdb
Description: Protein Databank data


443884.pdbqt
Description: Binary data
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[Open Babel] Error in file conversion

[Sundar]

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 data


443884.pdbqt
Description: Binary data
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[Open Babel] netcharge of a molecule

[Sundar]

Hi everyone,

How to calculate the net charge of a molecule in openbabel?

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

[Sundar]

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 used openbabel to do this. It worked mostly fine but with a few
> compounds, specially with the ones have protonated Nitrogen, gets destroyed.
>
> What exactly do you mean by "gets destroyed?" Being more specific, or
> ideally providing a file and/or graphic would be very helpful.
>
> Best regards,
> -Geoff
>
> ---
> Prof. Geoffrey Hutchison
> Department of Chemistry
> University of Pittsburgh
> tel: (412) 648-0492
> email: geo...@pitt.edu
> twitter: @ghutchis
> web: https://hutchison.chem.pitt.edu/


443884.pdb
Description: Protein Databank data


443884.pdbqt
Description: Binary data


443884.sdf
Description: Binary data
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[Open Babel] Best way to convert pdbqt to pdb

[Sundar]

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
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Re: [Open Babel] Aromaticity

[Sundar]

I usually convert SMILES to SDF.
In my current project, I didn't call the flag -aa. Would that have affected
the aromaticity of the compounds or the default attempt would have worked?
I didn't see any warnings about failing attempts to fix the aromaticity.

What's the general rule 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 <baoille...@gmail.com> wrote:

> HI Jubilant,
>
> The development version has rewritten handling of aromaticity, and as this
> will be the next release, I will focus on this. The following talk gives an
> overview of the process:
> https://baoilleach.blogspot.co.uk/2017/08/my-acs-talk-on-
> kekulization-and.html
>
> Your question didn't mention what conversion you are doing. When reading
> aromatic SMILES, we attempt to kekulize the aromatic bonds provided. If
> this is not possible, we don't fix it (which is not possible in the general
> case) - but instead produce a warning.
>
> When writing aromatic SMILES, we perceive aromaticity by default using the
> Daylight model described in the talk (to be exact, it's an extension of
> Daylight). If instead, you would like to use the aromaticity as present in
> the input SMILES, you can specify "-aa" when reading.
>
> Regards,
> - Noel
>
> On 1 December 2017 at 06:38, Sundar <jubilantsun...@gmail.com> wrote:
>
>> 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 the documentation page.
>>
>> Thanks,
>> Jubilant
>>
>> 
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[Open Babel] Obabel warning while pdb to sdf conversion

[Sundar]

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 HETATM or ATOM record.
  According to the PDB specification,
  columns 77-78 should contain the element symbol of an atom.
  but OpenBabel found '  ' (atom 1)
.
.
.
.
same error 32 times with (atom 1) to (atom 32). I was converting a total of
~8000 pdbs.

I don't have columns 77-78 in my pdbs.

Thanks,
Sundr
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[Open Babel] Aromaticity

[Sundar]

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 the documentation page.

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

[Sundar]

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

[Sundar]

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 <li...@cowsandmilk.net> wrote:

> Assuming you want the 9782’th molecule in the file, using the -f and -l
> options to obabel is what you are looking for.
>
> obabel ../input/in-3D.sdf -O 9782.sdf -f 9782 -l 9782
>
>
> > On Nov 5, 2017, at 7:49 PM, Sundar <jubilantsun...@gmail.com> wrote:
> >
> > 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
> > 
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[Open Babel] extract a single compound from a multimolecular sdf

[Sundar]

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

[Sundar]

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.
"*** Open Babel Warning  in CorrectStereoAtoms
  Could not correct 2 stereocenter(s) in this molecule (6674)
  with Atom Ids as follows: 7 9
Warning: Stereochemistry is wrong, using the distance geometry method
instead
"
The command I ran is
$ obabel 2D.sdf -O 3D.sdf --gen3d

But I still see 0. for z-coordinates for several compounds. Do you
still want those compounds to test yourself?

Thanks,
Jubilant

On Wed, Oct 25, 2017 at 9:39 AM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:

> > Are you able to provide files that show this? Or reduce it to single
> compounds that are being eliminated that can be shared?
>
> Even if it’s only a subset, that would be helpful.
>
> I’m working on a distance geometry method that should offer increased
> range. Either way, having examples is crucial.
>
> Thanks,
> -Geoff
>
>
>
> 
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Re: [Open Babel] single sdf to multi pdbs conversion with compound names

[Sundar]

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 <c.mor...@gaseq.co.uk> wrote:

> On 25/10/2017 07:55, Sundar wrote:
>
> 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?
>>
>
> Try:
>  obabel manymols.sdf -O dummy.pdb --split
>
> Each output file has a name in which 'dummy' is replaced by title of the
> molecule.
> (You can use -opdb to specify the output format, but OB uses the first
> extension for this format, which is .ent.)
>
> The output file name can also be made from other properties of the
> molecule.
>
> Read the description of --split:
>  obabel -L split
>
> Chris
>
>
> 
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[Open Babel] single sdf to multi pdbs conversion with compound names

[Sundar]

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

[Sundar]

Hi Geoff,

When I tried to convert a multimolecule pdb file (output from obminimize)
to an sdf file, only the first molecule was converted.
I wrote my own script to split the file into multiple pdbs and put them
together as single sdf using obabel.
But any solution using obabel to that in single step i.e. converting
multimolecular pdb to sdf?

Thanks,
Sundar

On Thu, Oct 19, 2017 at 8:01 PM, Sundar Jubilant <jubilantsun...@gmail.com>
wrote:

> Thanks. I will try that.
>
> Sundar Thangapandian
>
> > On Oct 19, 2017, at 6:40 PM, Geoffrey Hutchison <
> geoff.hutchi...@gmail.com> 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.sdf
> >
> >> 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?
> >
> > You can also use the --minimize flag with obabel to minimize molecules.
> > http://open-babel.readthedocs.io/en/latest/Command-line_
> tools/babel.html?highlight=minimize#forcefield-energy-and-minimization
> >
> > Hope that helps,
> > -Geoff
>
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Re: [Open Babel] obminimize outputs only in pdb (multimolecule pdb)

[Sundar Jubilant]

Thanks. I will try that.

Sundar Thangapandian

> On Oct 19, 2017, at 6:40 PM, Geoffrey Hutchison <geoff.hutchi...@gmail.com> 
> 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.sdf
> 
>> 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?
> 
> You can also use the --minimize flag with obabel to minimize molecules.
> http://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html?highlight=minimize#forcefield-energy-and-minimization
> 
> Hope that helps,
> -Geoff

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

[Sundar Jubilant]

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 required development libraries
> aren't already installed, setting it all up in your home directory is a
> major PITA. And you may run out of disk quotas etc.
> 
> To the OP: if that's the case, get a linux machine with root access.
> -- 
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
> 
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[Open Babel] building openbabel with no root access

[Sundar]

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

[Sundar Jubilant]

Yes. 

Sundar Thangapandian

> On Oct 13, 2017, at 3:08 PM, David Hall <li...@cowsandmilk.net> wrote:
> 
> I assume your second command is actually using output2D.sdf as input?
> 
> -David
> 
>> On Oct 13, 2017, at 3:46 PM, Sundar <jubilantsun...@gmail.com> wrote:
>> 
>> 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 2:18 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
>>> I'm a bit confused. Can you write out in full the commands you used?
>>> 
>>>> On 13 Oct 2017 6:53 p.m., "Sundar" <jubilantsun...@gmail.com> wrote:
>>>> Hi Noel,
>>>> 
>>>> No. I used --unique option to generate 2D coformations from smiles and got 
>>>> ~7000 compounds.
>>>> While generating 3D from the 2D I only used --gen3d
>>>> 
>>>> Thanks,
>>>> Jubilant
>>>> 
>>>>> On Fri, Oct 13, 2017 at 11:28 AM, Noel O'Boyle <baoille...@gmail.com> 
>>>>> wrote:
>>>>> Hi there,
>>>>> 
>>>>> The "--unique" option removes duplicates. My guess is that you have only 
>>>>> 800 unique compounds.
>>>>> 
>>>>> Regards,
>>>>> - Noel
>>>>> 
>>>>>> On 13 October 2017 at 11:58, Sundar <jubilantsun...@gmail.com> wrote:
>>>>>> 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 behaves this way?
>>>>>> 
>>>>>> -Jubilant
>>>>>> 
>>>>>> --
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>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>>>>>> 
>>>>> 
>>>> 
>> 
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Re: [Open Babel] gen3d doesn't convert all compounds

[Sundar]

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 2:18 PM, Noel O'Boyle <baoille...@gmail.com> wrote:

> I'm a bit confused. Can you write out in full the commands you used?
>
> On 13 Oct 2017 6:53 p.m., "Sundar" <jubilantsun...@gmail.com> wrote:
>
>> Hi Noel,
>>
>> No. I used --unique option to generate 2D coformations from smiles and
>> got ~7000 compounds.
>> While generating 3D from the 2D I only used --gen3d
>>
>> Thanks,
>> Jubilant
>>
>> On Fri, Oct 13, 2017 at 11:28 AM, Noel O'Boyle <baoille...@gmail.com>
>> wrote:
>>
>>> Hi there,
>>>
>>> The "--unique" option removes duplicates. My guess is that you have only
>>> 800 unique compounds.
>>>
>>> Regards,
>>> - Noel
>>>
>>> On 13 October 2017 at 11:58, Sundar <jubilantsun...@gmail.com> wrote:
>>>
>>>> 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 behaves this way?
>>>>
>>>> -Jubilant
>>>>
>>>> 
>>>> --
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>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>>>>
>>>>
>>>
>>
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[Open Babel] obminimize outputs only in pdb (multimolecule pdb)

[Sundar]

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

[Sundar]

Hi Noel,

No. I used --unique option to generate 2D coformations from smiles and got
~7000 compounds.
While generating 3D from the 2D I only used --gen3d

Thanks,
Jubilant

On Fri, Oct 13, 2017 at 11:28 AM, Noel O'Boyle <baoille...@gmail.com> wrote:

> Hi there,
>
> The "--unique" option removes duplicates. My guess is that you have only
> 800 unique compounds.
>
> Regards,
> - Noel
>
> On 13 October 2017 at 11:58, Sundar <jubilantsun...@gmail.com> wrote:
>
>> 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 behaves this way?
>>
>> -Jubilant
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
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>
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[Open Babel] gen3d doesn't convert all compounds

[Sundar]

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 behaves this way?

-Jubilant
--
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engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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https://lists.sourceforge.net/lists/listinfo/openbabel-discuss