[Open Babel] aromaticity depends on atom order in PDB file
Hello I am using version 2.4.1 and run in the following issue: when I convert the following PDB file to mol2 the atoms in the rings are aromatic REMARK AtomGroup 3got_lig HETATM 1 N1 A2F A 91 -12.060 -9.865 9.375 1.00 34.52 N HETATM 2 C2 A2F A 91 -11.647 -11.140 9.446 1.00 36.07 C HETATM 3 N3 A2F A 91 -11.218 -11.795 8.356 1.00 35.26 N HETATM 4 C4 A2F A 91 -11.199 -11.188 7.163 1.00 34.93 C HETATM 5 C5 A2F A 91 -11.626 -9.872 7.057 1.00 34.33 C HETATM 6 C6 A2F A 91 -12.054 -9.212 8.203 1.00 34.11 C HETATM 7 N6 A2F A 91 -12.392 -7.927 8.148 1.00 31.63 N HETATM 8 N7 A2F A 91 -11.502 -9.521 5.780 1.00 34.42 N HETATM 9 C8 A2F A 91 -11.013 -10.561 5.109 1.00 34.57 C HETATM 10 N9 A2F A 91 -10.826 -11.579 5.948 1.00 34.76 N HETATM 11 F A2F A 91 -11.661 -11.789 10.626 1.00 35.98 F but if the atom order is changed HETATM 1 F A2F A 91 -11.661 -11.789 10.626 1.00 35.98 F HETATM 2 C2 A2F A 91 -11.647 -11.140 9.446 1.00 36.07 C HETATM 3 N3 A2F A 91 -11.218 -11.795 8.356 1.00 35.26 N HETATM 4 N1 A2F A 91 -12.060 -9.865 9.375 1.00 34.52 N HETATM 5 C6 A2F A 91 -12.054 -9.212 8.203 1.00 34.11 C HETATM 6 N6 A2F A 91 -12.392 -7.927 8.148 1.00 31.63 N HETATM 7 C5 A2F A 91 -11.626 -9.872 7.057 1.00 34.33 C HETATM 8 C4 A2F A 91 -11.199 -11.188 7.163 1.00 34.93 C HETATM 9 N7 A2F A 91 -11.502 -9.521 5.780 1.00 34.42 N HETATM 10 C8 A2F A 91 -11.013 -10.561 5.109 1.00 34.57 C HETATM 11 N9 A2F A 91 -10.826 -11.579 5.948 1.00 34.76 N none of the atoms or bonds is aromatic -Michel ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] obminimize stop criteria
Dear all, I am having some troubles in get some (supposedly straightforward) relaxations results. I want to relax a benzene molecule in xyz format (this is a test for more complex results). I tried both "obminimize" and "obabel --minimize", compiling the source code and the anaconda3 version. In all cases I do get a different geometry with lower energy, but I can neither get the code to stop when the criteria is reached nor obtain a convergence message whatsoever. $ obabel benzene.xyz -O min_benzene.xyz --minimize --steps 500 --sd --ff UFF --log --crit 1e-4 ## --crit 1e0 gives the same result, log_001.txt $ obminimize benzene.xyz -O min_benzene.xyz --steps 500 --sd --ff UFF --crit 1e-4 In addition, In the obminimize case, I get an error message, zero charges and alternate +/- 0.15 partial charges, as shown below. ''' *** Open Babel Warning in ReadMolecule Problems reading an XYZ file: Cannot read the first line. ''' IDX CHARGE 1 0.00 ... 12 0.00 P A R T I A L C H A R G E S IDX CHARGE 1 -0.15 2 0.15 ... Could anyone explain what am I doing wrong? Thank you Marco Marco Di Gennaro Toyota Motor Europe This e-mail may contain confidential information. If you are not an addressee or otherwise authorised to receive this message, you should not use, copy, disclose or take any action based on this e-mail. If you have received this e-mail in error, please inform the sender promptly and delete this message and any attachments immediately. 12 benzene example C0.01.402720.0 H0.02.490290.0 C -1.214790.701360.0 H -2.156661.245150.0 C -1.21479 -0.701360.0 H -2.15666 -1.245150.0 C0.0 -1.402720.0 H0.0 -2.490290.0 C1.21479 -0.701360.0 H2.15666 -1.245150.0 C1.214790.701360.0 H2.156661.245150.0 A T O M T Y P E S IDX TYPERING 1 C_R AR 2 H_ NO 3 C_R AR 4 H_ NO 5 C_R AR 6 H_ NO 7 C_R AR 8 H_ NO 9 C_R AR 10 H_ NO 11 C_R AR 12 H_ NO S E T T I N G U P C A L C U L A T I O N S SETTING UP BOND CALCULATIONS... SETTING UP ANGLE CALCULATIONS... SETTING UP TORSION CALCULATIONS... SETTING UP OOP CALCULATIONS... SETTING UP VAN DER WAALS CALCULATIONS... S T E E P E S T D E S C E N T STEPS = 50 STEP n E(n) E(n-1) 0 44.709 1044.2700844.27014 2044.2699744.26997 3044.2699744.26997 4044.2699744.26997 5044.2699744.26997 ... 50044.2699744.26997 ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] compiling python bindings for obabel 3.0
Yes 3.0. E.g. from https://github.com/openbabel/openbabel/releases On Thu, 16 Apr 2020 at 21:25, Bennion, Brian wrote: > Is there a later version than 2.3.1.tar.gz that I can download? > -- > *From:* Noel O'Boyle > *Sent:* Thursday, April 16, 2020 1:16 PM > *To:* Bennion, Brian > *Cc:* openbabel-discuss@lists.sourceforge.net < > openbabel-discuss@lists.sourceforge.net> > *Subject:* Re: compiling python bindings for obabel 3.0 > > If you use CMAKE_INSTALL_PREFIX=wherever, then the Python bindings will be > installed locally, along with the rest of Open Babel. There is no need for > Conda or pip, etc. Are you saying that this wouldn't work for you for some > reason? To use it, you just need to set a couple of environment variables. > > - Noel > > On Thu, 16 Apr 2020 at 21:03, Bennion, Brian wrote: > > I would love to edit the the subject line but outlook online does not > offer that option that I can find so I am starting a new thread. > > The issue we have is that unless I want to have my own personally managed > and updated python installation (not using our LC compute clusters) the > current install regime will not work as it tries to modify site package > directories that I have no write access to. > > I would like to have our LC people support this directly so all users have > access to the tool, but that is not an option right now. > > so my options are not use python bindings, a pain in the neck > create some virtual environment like conda or pip for myself and then > everyone else has to have access to it or build their own env. > > Other options? > brian > > > ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
