[Open Babel] Open Babel Gasteiger partial charges and the -p option

2018-06-18 Thread MichaelSmith 
Hi,

According to the 2006 J Comput Chem paper describing Autodock 4, OpenBabel
was used to add hydrogens and assign Gasteiger charges to the protein and
ligands that were used as the training set to calibrate the force field. I
just want to ask whether the -p option in OB was used to do this (where it
allows the user to specify a pH so that it can attempt to calculate
protonation states). There has been a bug discovered in this usage of
OpenBabel where very large charges can get assigned to molecules. I have
seen one example of a small molecule being assigned a total charge of -9,
when it reality it contains a single ionizable group.Can someone please
comment on whether this might have had an impact on the accuracy of
Autodock's force field?


Please help.

I didn't find the right solution from the Internet.

References:-
http://mgl.scripps.edu/forum/viewtopic.php?f=9&t=1398
Custom Video Creation Service
  

Thanks!





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[Open Babel] Error on installing openbabel-2.4.1

2018-06-18 Thread Yang, Chengxi 
Dear Openbabel Stuff,

I am having trouble installing openbabel-2.4.1 with C# binding.
Specifically, after the *Cmake* step, I run *make install*, then the error
happens.
At the end of the installation, it says:

[100%] *Linking CXX executable ../bin/test_runner*

[100%] Built target test_runner

[100%] *Generating
/Users/chengxiyang/Downloads/openbabel-2.4.1/scripts/csharp/openbabel-csharp.cpp,
/Users/chengxiyang/Downloads/openbabel-2.4.1/scripts/csharp/OBDotNet.dll*

Cannot open assembly '/target:library': No such file or directory.

make[2]: ***
[/Users/chengxiyang/Downloads/openbabel-2.4.1/scripts/csharp/openbabel-csharp.cpp]
Error 2

make[2]: *** Deleting file
`/Users/chengxiyang/Downloads/openbabel-2.4.1/scripts/csharp/openbabel-csharp.cpp'

make[1]: *** [scripts/CMakeFiles/bindings_csharp.dir/all] Error 2

make: *** [all] Error 2


I am using MacOS and here is my system information:


*Hardware Overview:*


  Model Name: MacBook Pro

  Model Identifier: MacBookPro13,3

  Processor Name: Intel Core i7

  Processor Speed: 2.6 GHz

  Number of Processors: 1

  Total Number of Cores: 4

  L2 Cache (per Core): 256 KB

  L3 Cache: 6 MB

  Memory: 16 GB

  Boot ROM Version: MBP133.0242.B00

  SMC Version (system): 2.38f7

  Serial Number (system): C02T90B2H03M

  Hardware UUID: DE3C82F1-E62B-5AEE-AD10-C95E201D62AE



*System Software Overview:*


  System Version: macOS 10.13.4 (17E202)

  Kernel Version: Darwin 17.5.0

  Boot Volume: Macintosh HD

  Boot Mode: Normal

  Computer Name: Chengxi’s MacBook Pro

  User Name: Chengxi Yang (chengxiyang)

  Secure Virtual Memory: Enabled

  System Integrity Protection: Enabled

  Time since boot: 1 day 1:48



Here is the command I run *cmake**:*


*cmake ../openbabel-2.4.1 -DCSHARP_BINDINGS=ON
-DCSHARP_EXECUTABLE=/Library/Frameworks/Mono.framework/Versions/Current/bin/mono
-DRUN_SWIG=ON *



I have attach the output of *cmake* and *make install *in the attachment
file.

Thank you for taking a look at it and I will really appreciate you help.


Best,

Chengxi
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Re: [Open Babel] Error on installing openbabel-2.4.1

2018-06-18 Thread Noel O'Boyle 
The code is targeting the Windows .NET platform. Try altering the
appropriate lines in scripts/CMakeLists.txt so that the command-line
parameters are appropriate for Mono. For example, trying openbabel-mono.i
instead of openbabel-csharp.i. Also try "-target:library" instead of
"/target:library", and so forth. If you figure it out, let us know, and
we'll update the build so that Mono is supported out-of-the-box. It has
worked in the past but nobody has been interested in that for a while.

- Noel




On 14 June 2018 at 23:57, Yang, Chengxi  wrote:

> Dear Openbabel Stuff,
>
> I am having trouble installing openbabel-2.4.1 with C# binding.
> Specifically, after the *Cmake* step, I run *make install*, then the
> error happens.
> At the end of the installation, it says:
>
> [100%] *Linking CXX executable ../bin/test_runner*
>
> [100%] Built target test_runner
>
> [100%] *Generating
> /Users/chengxiyang/Downloads/openbabel-2.4.1/scripts/csharp/openbabel-csharp.cpp,
> /Users/chengxiyang/Downloads/openbabel-2.4.1/scripts/csharp/OBDotNet.dll*
>
> Cannot open assembly '/target:library': No such file or directory.
>
> make[2]: *** 
> [/Users/chengxiyang/Downloads/openbabel-2.4.1/scripts/csharp/openbabel-csharp.cpp]
> Error 2
>
> make[2]: *** Deleting file `/Users/chengxiyang/Downloads/
> openbabel-2.4.1/scripts/csharp/openbabel-csharp.cpp'
>
> make[1]: *** [scripts/CMakeFiles/bindings_csharp.dir/all] Error 2
>
> make: *** [all] Error 2
>
>
> I am using MacOS and here is my system information:
>
>
> *Hardware Overview:*
>
>
>   Model Name: MacBook Pro
>
>   Model Identifier: MacBookPro13,3
>
>   Processor Name: Intel Core i7
>
>   Processor Speed: 2.6 GHz
>
>   Number of Processors: 1
>
>   Total Number of Cores: 4
>
>   L2 Cache (per Core): 256 KB
>
>   L3 Cache: 6 MB
>
>   Memory: 16 GB
>
>   Boot ROM Version: MBP133.0242.B00
>
>   SMC Version (system): 2.38f7
>
>   Serial Number (system): C02T90B2H03M
>
>   Hardware UUID: DE3C82F1-E62B-5AEE-AD10-C95E201D62AE
>
>
>
> *System Software Overview:*
>
>
>   System Version: macOS 10.13.4 (17E202)
>
>   Kernel Version: Darwin 17.5.0
>
>   Boot Volume: Macintosh HD
>
>   Boot Mode: Normal
>
>   Computer Name: Chengxi’s MacBook Pro
>
>   User Name: Chengxi Yang (chengxiyang)
>
>   Secure Virtual Memory: Enabled
>
>   System Integrity Protection: Enabled
>
>   Time since boot: 1 day 1:48
>
>
>
> Here is the command I run *cmake**:*
>
>
> *cmake ../openbabel-2.4.1 -DCSHARP_BINDINGS=ON
> -DCSHARP_EXECUTABLE=/Library/Frameworks/Mono.framework/Versions/Current/bin/mono
> -DRUN_SWIG=ON *
>
>
>
> I have attach the output of *cmake* and *make install *in the attachment
> file.
>
> Thank you for taking a look at it and I will really appreciate you help.
>
>
> Best,
>
> Chengxi
>
>
>
> 
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> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> OpenBabel-discuss mailing list
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> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
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