Atom numbering unification

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Atom numbering unification

Dmitry Osolodkin-2
Hello OpenBabel developers and users,

probably you could help me with a simple problem. I have two molecules
(attached) to compute all-atom RMSD between them; they are same at all
except the position in the space (docking result and a cocrystal
structure). The only problem is that they have different atom numbering,
so RMSD-computing tools using atom numbers such as VMD RMSD Calculator
plugin give unreasonable numbers (about 5 A in this case, which is
obviously wrong).

The question is: is it possible to change only atom numbering in one or
both molecules to make it the same for them, e.g. canonical? Or one of
them can be used as a template? Manual correction is hardly acceptable
because I have a series of complexes, not one. I also don't need
translation or rotation of the molecules, just compute RMSD between the
given positions.

Thanks in advance,
Dmitry Osolodkin
--
Dmitry Osolodkin
Researcher
Group of Computational Molecular Design
Department of Chemistry
Moscow State University
Moscow 119991 Russia
e-mail: [hidden email]
Phone: +7-495-9393557
Fax: +7-495-9390290

------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
OpenBabel-discuss mailing list
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https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

1UV5_docked.mol2 (3K) Download Attachment
1UV5_extract.mol2 (4K) Download Attachment
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Re: Atom numbering unification

Tim Vandermeersch
Hi,

2010/9/23 Dmitry Osolodkin <[hidden email]>:

> Hello OpenBabel developers and users,
>
> probably you could help me with a simple problem. I have two molecules
> (attached) to compute all-atom RMSD between them; they are same at all
> except the position in the space (docking result and a cocrystal
> structure). The only problem is that they have different atom numbering,
> so RMSD-computing tools using atom numbers such as VMD RMSD Calculator
> plugin give unreasonable numbers (about 5 A in this case, which is
> obviously wrong).
>
> The question is: is it possible to change only atom numbering in one or
> both molecules to make it the same for them, e.g. canonical? Or one of
> them can be used as a template? Manual correction is hardly acceptable
> because I have a series of complexes, not one. I also don't need
> translation or rotation of the molecules, just compute RMSD between the
> given positions.

If you are willing to try the development version, you can
canonicalize the atom order for any format using:

babel --canonical somefile.mol2 somefile_can.mol2

Tim

> Thanks in advance,
> Dmitry Osolodkin
> --
> Dmitry Osolodkin
> Researcher
> Group of Computational Molecular Design
> Department of Chemistry
> Moscow State University
> Moscow 119991 Russia
> e-mail: [hidden email]
> Phone: +7-495-9393557
> Fax: +7-495-9390290
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>

------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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Re: Atom numbering unification

Dmitry Osolodkin-2
Hi Tim,

On 09/24/2010 02:20 PM, Tim Vandermeersch wrote:
> If you are willing to try the development version, you can
> canonicalize the atom order for any format using:
>
> babel --canonical somefile.mol2 somefile_can.mol2

It doesn't work. Atom order remains the same as in input files. Using
the latest development version or stable 2.2.3 -- no difference.

Dmitry.
--
Dmitry Osolodkin
Researcher
Group of Computational Molecular Design
Department of Chemistry
Moscow State University
Moscow 119991 Russia
e-mail: [hidden email]
Phone: +7-495-9393557
Fax: +7-495-9390290


------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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Re: Atom numbering unification

Tim Vandermeersch
2010/9/24 Dmitry Osolodkin <[hidden email]>:

> Hi Tim,
>
> On 09/24/2010 02:20 PM, Tim Vandermeersch wrote:
>> If you are willing to try the development version, you can
>> canonicalize the atom order for any format using:
>>
>> babel --canonical somefile.mol2 somefile_can.mol2
>
> It doesn't work. Atom order remains the same as in input files. Using
> the latest development version or stable 2.2.3 -- no difference.

Make sure to run make install or use ./bin/babel, otherwise you are
just using the older installed version. It works on your example files
here.

> Dmitry.
> --
> Dmitry Osolodkin
> Researcher
> Group of Computational Molecular Design
> Department of Chemistry
> Moscow State University
> Moscow 119991 Russia
> e-mail: [hidden email]
> Phone: +7-495-9393557
> Fax: +7-495-9390290
>
>

------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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Re: Atom numbering unification

Dmitry Osolodkin-2
On 09/24/2010 04:08 PM, Tim Vandermeersch wrote:
>>> babel --canonical somefile.mol2 somefile_can.mol2
>>
>> It doesn't work. Atom order remains the same as in input files. Using
>> the latest development version or stable 2.2.3 -- no difference.
>
> Make sure to run make install or use ./bin/babel, otherwise you are
> just using the older installed version. It works on your example files
> here.

I have checked everything, but atom order is still different even for
these files (see attachment). Development version:

> which babel
/usr/local/openbabel/bin/babel

> echo $LD_LIBRARY_PATH
/usr/lib/mpi/gcc/openmpi/lib:/opt/intel_fc_80/lib:/opt/intel/mkl/10.1.1.019/lib/32::/opt/intel_fc_80/lib:/opt/intel/mkl/10.1.1.019/lib/32:/usr/local/openbabel/lib


> babel --canonical 1UV5_extract.mol2 1UV5_extract_can.mol2 ---errorlevel 5
==============================
*** Open Babel Audit Log  in ReadChemObjectImpl
  OpenBabel::Read molecule Sybyl Mol2 format
==============================
*** Open Babel Audit Log  in Clear
  Ran OpenBabel::Clear Molecule
==============================
*** Open Babel Audit Log  in Kekulize
  Ran OpenBabel::Kekulize
==============================
*** Open Babel Audit Log  in FindSSSR
  Ran OpenBabel::FindSSSR
==============================
*** Open Babel Audit Log  in FindRingAtomsAndBonds
  Ran OpenBabel::FindRingAtomsAndBonds
==============================
*** Open Babel Audit Log  in IsClosure
  Ran OpenBabel::PerceiveClosureBonds
==============================
*** Open Babel Audit Log  in FindLSSR
  Ran OpenBabel::FindLSSR
==============================
*** Open Babel Audit Log  in ReadChemObjectImpl
  OpenBabel::Read molecule Sybyl Mol2 format
==============================
*** Open Babel Audit Log  in Clear
  Ran OpenBabel::Clear Molecule
==============================
*** Open Babel Audit Log  in WriteChemObjectImpl
  OpenBabel::Write molecule Sybyl Mol2 format
==============================
*** Open Babel Audit Log  in AssignTypes
  Ran OpenBabel::AssignTypes
==============================
*** Open Babel Audit Log  in AssignAromaticFlags
  Ran OpenBabel::AssignAromaticFlags
==============================
*** Open Babel Audit Log  in AssignImplicitValence
  Ran OpenBabel::AssignImplicitValence
==============================
*** Open Babel Audit Log  in AssignHyb
  Ran OpenBabel::AssignHybridization
==============================
*** Open Babel Audit Log  in AssignHyb
  Ran OpenBabel::AssignHybridization
1 molecule converted
15 audit log messages


> babel --canonical 1UV5_docked.mol2 1UV5_docked_can.mol2 ---errorlevel 5
==============================
*** Open Babel Audit Log  in ReadChemObjectImpl
  OpenBabel::Read molecule Sybyl Mol2 format
==============================
*** Open Babel Audit Log  in Clear
  Ran OpenBabel::Clear Molecule
==============================
*** Open Babel Audit Log  in Kekulize
  Ran OpenBabel::Kekulize
==============================
*** Open Babel Audit Log  in FindSSSR
  Ran OpenBabel::FindSSSR
==============================
*** Open Babel Audit Log  in FindRingAtomsAndBonds
  Ran OpenBabel::FindRingAtomsAndBonds
==============================
*** Open Babel Audit Log  in IsClosure
  Ran OpenBabel::PerceiveClosureBonds
==============================
*** Open Babel Audit Log  in FindLSSR
  Ran OpenBabel::FindLSSR
==============================
*** Open Babel Audit Log  in ReadChemObjectImpl
  OpenBabel::Read molecule Sybyl Mol2 format
==============================
*** Open Babel Audit Log  in Clear
  Ran OpenBabel::Clear Molecule
==============================
*** Open Babel Audit Log  in WriteChemObjectImpl
  OpenBabel::Write molecule Sybyl Mol2 format
==============================
*** Open Babel Audit Log  in AssignTypes
  Ran OpenBabel::AssignTypes
==============================
*** Open Babel Audit Log  in AssignAromaticFlags
  Ran OpenBabel::AssignAromaticFlags
==============================
*** Open Babel Audit Log  in AssignImplicitValence
  Ran OpenBabel::AssignImplicitValence
==============================
*** Open Babel Audit Log  in AssignHyb
  Ran OpenBabel::AssignHybridization
==============================
*** Open Babel Audit Log  in AssignHyb
  Ran OpenBabel::AssignHybridization
==============================
*** Open Babel Audit Log  in PerceiveChains
  Ran OpenBabel::PerceiveChains
==============================
*** Open Babel Information  in ParseLine
   Could not parse line in phmodel table from phmodel.txt
==============================
*** Open Babel Audit Log  in AssignPartialCharges
  Ran OpenBabel::AssignPartialCharges
1 molecule converted
1 info messages 17 audit log messages



--
Dmitry Osolodkin
Researcher
Group of Computational Molecular Design
Department of Chemistry
Moscow State University
Moscow 119991 Russia
e-mail: [hidden email]
Phone: +7-495-9393557
Fax: +7-495-9390290

------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

1UV5_docked_can.mol2 (3K) Download Attachment
1UV5_extract_can.mol2 (3K) Download Attachment
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Re: Atom numbering unification

Tim Vandermeersch
2010/9/24 Dmitry Osolodkin <[hidden email]>:

> On 09/24/2010 04:08 PM, Tim Vandermeersch wrote:
>>>> babel --canonical somefile.mol2 somefile_can.mol2
>>>
>>> It doesn't work. Atom order remains the same as in input files. Using
>>> the latest development version or stable 2.2.3 -- no difference.
>>
>> Make sure to run make install or use ./bin/babel, otherwise you are
>> just using the older installed version. It works on your example files
>> here.
>
> I have checked everything, but atom order is still different even for
> these files (see attachment). Development version:

Sorry, I forgot to commit the changes to the build system. It's in svn
now. You can verify that the --canonical option is present by running
"babel -H", it should be in the list now.

Tim

>> which babel
> /usr/local/openbabel/bin/babel
>
>> echo $LD_LIBRARY_PATH
> /usr/lib/mpi/gcc/openmpi/lib:/opt/intel_fc_80/lib:/opt/intel/mkl/10.1.1.019/lib/32::/opt/intel_fc_80/lib:/opt/intel/mkl/10.1.1.019/lib/32:/usr/local/openbabel/lib
>
>
>> babel --canonical 1UV5_extract.mol2 1UV5_extract_can.mol2 ---errorlevel 5
> ==============================
> *** Open Babel Audit Log  in ReadChemObjectImpl
>  OpenBabel::Read molecule Sybyl Mol2 format
> ==============================
> *** Open Babel Audit Log  in Clear
>  Ran OpenBabel::Clear Molecule
> ==============================
> *** Open Babel Audit Log  in Kekulize
>  Ran OpenBabel::Kekulize
> ==============================
> *** Open Babel Audit Log  in FindSSSR
>  Ran OpenBabel::FindSSSR
> ==============================
> *** Open Babel Audit Log  in FindRingAtomsAndBonds
>  Ran OpenBabel::FindRingAtomsAndBonds
> ==============================
> *** Open Babel Audit Log  in IsClosure
>  Ran OpenBabel::PerceiveClosureBonds
> ==============================
> *** Open Babel Audit Log  in FindLSSR
>  Ran OpenBabel::FindLSSR
> ==============================
> *** Open Babel Audit Log  in ReadChemObjectImpl
>  OpenBabel::Read molecule Sybyl Mol2 format
> ==============================
> *** Open Babel Audit Log  in Clear
>  Ran OpenBabel::Clear Molecule
> ==============================
> *** Open Babel Audit Log  in WriteChemObjectImpl
>  OpenBabel::Write molecule Sybyl Mol2 format
> ==============================
> *** Open Babel Audit Log  in AssignTypes
>  Ran OpenBabel::AssignTypes
> ==============================
> *** Open Babel Audit Log  in AssignAromaticFlags
>  Ran OpenBabel::AssignAromaticFlags
> ==============================
> *** Open Babel Audit Log  in AssignImplicitValence
>  Ran OpenBabel::AssignImplicitValence
> ==============================
> *** Open Babel Audit Log  in AssignHyb
>  Ran OpenBabel::AssignHybridization
> ==============================
> *** Open Babel Audit Log  in AssignHyb
>  Ran OpenBabel::AssignHybridization
> 1 molecule converted
> 15 audit log messages
>
>
>> babel --canonical 1UV5_docked.mol2 1UV5_docked_can.mol2 ---errorlevel 5
> ==============================
> *** Open Babel Audit Log  in ReadChemObjectImpl
>  OpenBabel::Read molecule Sybyl Mol2 format
> ==============================
> *** Open Babel Audit Log  in Clear
>  Ran OpenBabel::Clear Molecule
> ==============================
> *** Open Babel Audit Log  in Kekulize
>  Ran OpenBabel::Kekulize
> ==============================
> *** Open Babel Audit Log  in FindSSSR
>  Ran OpenBabel::FindSSSR
> ==============================
> *** Open Babel Audit Log  in FindRingAtomsAndBonds
>  Ran OpenBabel::FindRingAtomsAndBonds
> ==============================
> *** Open Babel Audit Log  in IsClosure
>  Ran OpenBabel::PerceiveClosureBonds
> ==============================
> *** Open Babel Audit Log  in FindLSSR
>  Ran OpenBabel::FindLSSR
> ==============================
> *** Open Babel Audit Log  in ReadChemObjectImpl
>  OpenBabel::Read molecule Sybyl Mol2 format
> ==============================
> *** Open Babel Audit Log  in Clear
>  Ran OpenBabel::Clear Molecule
> ==============================
> *** Open Babel Audit Log  in WriteChemObjectImpl
>  OpenBabel::Write molecule Sybyl Mol2 format
> ==============================
> *** Open Babel Audit Log  in AssignTypes
>  Ran OpenBabel::AssignTypes
> ==============================
> *** Open Babel Audit Log  in AssignAromaticFlags
>  Ran OpenBabel::AssignAromaticFlags
> ==============================
> *** Open Babel Audit Log  in AssignImplicitValence
>  Ran OpenBabel::AssignImplicitValence
> ==============================
> *** Open Babel Audit Log  in AssignHyb
>  Ran OpenBabel::AssignHybridization
> ==============================
> *** Open Babel Audit Log  in AssignHyb
>  Ran OpenBabel::AssignHybridization
> ==============================
> *** Open Babel Audit Log  in PerceiveChains
>  Ran OpenBabel::PerceiveChains
> ==============================
> *** Open Babel Information  in ParseLine
>   Could not parse line in phmodel table from phmodel.txt
> ==============================
> *** Open Babel Audit Log  in AssignPartialCharges
>  Ran OpenBabel::AssignPartialCharges
> 1 molecule converted
> 1 info messages 17 audit log messages
>
>
>
> --
> Dmitry Osolodkin
> Researcher
> Group of Computational Molecular Design
> Department of Chemistry
> Moscow State University
> Moscow 119991 Russia
> e-mail: [hidden email]
> Phone: +7-495-9393557
> Fax: +7-495-9390290
>
------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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Re: Atom numbering unification

Dmitry Osolodkin-2
Thank you Tim, works fine now.

Best regards,
Dmitry.

On 09/24/2010 04:58 PM, Tim Vandermeersch wrote:

> 2010/9/24 Dmitry Osolodkin <[hidden email]>:
>> On 09/24/2010 04:08 PM, Tim Vandermeersch wrote:
>>>>> babel --canonical somefile.mol2 somefile_can.mol2
>>>>
>>>> It doesn't work. Atom order remains the same as in input files. Using
>>>> the latest development version or stable 2.2.3 -- no difference.
>>>
>>> Make sure to run make install or use ./bin/babel, otherwise you are
>>> just using the older installed version. It works on your example files
>>> here.
>>
>> I have checked everything, but atom order is still different even for
>> these files (see attachment). Development version:
>
> Sorry, I forgot to commit the changes to the build system. It's in svn
> now. You can verify that the --canonical option is present by running
> "babel -H", it should be in the list now.
>
> Tim
>
>>> which babel
>> /usr/local/openbabel/bin/babel
>>
>>> echo $LD_LIBRARY_PATH
>> /usr/lib/mpi/gcc/openmpi/lib:/opt/intel_fc_80/lib:/opt/intel/mkl/10.1.1.019/lib/32::/opt/intel_fc_80/lib:/opt/intel/mkl/10.1.1.019/lib/32:/usr/local/openbabel/lib
>>
>>
>>> babel --canonical 1UV5_extract.mol2 1UV5_extract_can.mol2 ---errorlevel 5
>> ==============================
>> *** Open Babel Audit Log  in ReadChemObjectImpl
>>  OpenBabel::Read molecule Sybyl Mol2 format
>> ==============================
>> *** Open Babel Audit Log  in Clear
>>  Ran OpenBabel::Clear Molecule
>> ==============================
>> *** Open Babel Audit Log  in Kekulize
>>  Ran OpenBabel::Kekulize
>> ==============================
>> *** Open Babel Audit Log  in FindSSSR
>>  Ran OpenBabel::FindSSSR
>> ==============================
>> *** Open Babel Audit Log  in FindRingAtomsAndBonds
>>  Ran OpenBabel::FindRingAtomsAndBonds
>> ==============================
>> *** Open Babel Audit Log  in IsClosure
>>  Ran OpenBabel::PerceiveClosureBonds
>> ==============================
>> *** Open Babel Audit Log  in FindLSSR
>>  Ran OpenBabel::FindLSSR
>> ==============================
>> *** Open Babel Audit Log  in ReadChemObjectImpl
>>  OpenBabel::Read molecule Sybyl Mol2 format
>> ==============================
>> *** Open Babel Audit Log  in Clear
>>  Ran OpenBabel::Clear Molecule
>> ==============================
>> *** Open Babel Audit Log  in WriteChemObjectImpl
>>  OpenBabel::Write molecule Sybyl Mol2 format
>> ==============================
>> *** Open Babel Audit Log  in AssignTypes
>>  Ran OpenBabel::AssignTypes
>> ==============================
>> *** Open Babel Audit Log  in AssignAromaticFlags
>>  Ran OpenBabel::AssignAromaticFlags
>> ==============================
>> *** Open Babel Audit Log  in AssignImplicitValence
>>  Ran OpenBabel::AssignImplicitValence
>> ==============================
>> *** Open Babel Audit Log  in AssignHyb
>>  Ran OpenBabel::AssignHybridization
>> ==============================
>> *** Open Babel Audit Log  in AssignHyb
>>  Ran OpenBabel::AssignHybridization
>> 1 molecule converted
>> 15 audit log messages
>>
>>
>>> babel --canonical 1UV5_docked.mol2 1UV5_docked_can.mol2 ---errorlevel 5
>> ==============================
>> *** Open Babel Audit Log  in ReadChemObjectImpl
>>  OpenBabel::Read molecule Sybyl Mol2 format
>> ==============================
>> *** Open Babel Audit Log  in Clear
>>  Ran OpenBabel::Clear Molecule
>> ==============================
>> *** Open Babel Audit Log  in Kekulize
>>  Ran OpenBabel::Kekulize
>> ==============================
>> *** Open Babel Audit Log  in FindSSSR
>>  Ran OpenBabel::FindSSSR
>> ==============================
>> *** Open Babel Audit Log  in FindRingAtomsAndBonds
>>  Ran OpenBabel::FindRingAtomsAndBonds
>> ==============================
>> *** Open Babel Audit Log  in IsClosure
>>  Ran OpenBabel::PerceiveClosureBonds
>> ==============================
>> *** Open Babel Audit Log  in FindLSSR
>>  Ran OpenBabel::FindLSSR
>> ==============================
>> *** Open Babel Audit Log  in ReadChemObjectImpl
>>  OpenBabel::Read molecule Sybyl Mol2 format
>> ==============================
>> *** Open Babel Audit Log  in Clear
>>  Ran OpenBabel::Clear Molecule
>> ==============================
>> *** Open Babel Audit Log  in WriteChemObjectImpl
>>  OpenBabel::Write molecule Sybyl Mol2 format
>> ==============================
>> *** Open Babel Audit Log  in AssignTypes
>>  Ran OpenBabel::AssignTypes
>> ==============================
>> *** Open Babel Audit Log  in AssignAromaticFlags
>>  Ran OpenBabel::AssignAromaticFlags
>> ==============================
>> *** Open Babel Audit Log  in AssignImplicitValence
>>  Ran OpenBabel::AssignImplicitValence
>> ==============================
>> *** Open Babel Audit Log  in AssignHyb
>>  Ran OpenBabel::AssignHybridization
>> ==============================
>> *** Open Babel Audit Log  in AssignHyb
>>  Ran OpenBabel::AssignHybridization
>> ==============================
>> *** Open Babel Audit Log  in PerceiveChains
>>  Ran OpenBabel::PerceiveChains
>> ==============================
>> *** Open Babel Information  in ParseLine
>>   Could not parse line in phmodel table from phmodel.txt
>> ==============================
>> *** Open Babel Audit Log  in AssignPartialCharges
>>  Ran OpenBabel::AssignPartialCharges
>> 1 molecule converted
>> 1 info messages 17 audit log messages
>>
>>
>>
>> --
>> Dmitry Osolodkin
>> Researcher
>> Group of Computational Molecular Design
>> Department of Chemistry
>> Moscow State University
>> Moscow 119991 Russia
>> e-mail: [hidden email]
>> Phone: +7-495-9393557
>> Fax: +7-495-9390290
>>

--
Dmitry Osolodkin
Researcher
Group of Computational Molecular Design
Department of Chemistry
Moscow State University
Moscow 119991 Russia
e-mail: [hidden email]
Phone: +7-495-9393557
Fax: +7-495-9390290


------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss