Re: [Open Babel] Conformer searching
Thanks Igor but that was just an example of how you could find the minima from input structures, I am interested in generating the conformers using openbabel. Best wishes, Scott On 20 March 2014 15:21, Igor Filippov igor.v.filip...@gmail.com wrote: I don't think openbabel can do DFT or any kind of ab initio quantum chemistry. Regards, Igor On Thu, Mar 20, 2014 at 11:15 AM, Scott McKechnie js...@cam.ac.uk wrote: Ethane (C2H6) and hydrazine (N2H4) have distinct minima that are separated by rotational barriers. Depending on the input structure, a geometry optimization (for instance in DFT) will bring you to one of these minima. I am interested in generating such conformations in a systematic way. Best wishes. Scott On 20 March 2014 15:06, Igor Filippov igor.v.filip...@gmail.com wrote: Hold on, what is to rotate in a C2 or N2 molecule? And what would be a conformation for a diatomic structure aside from the trivial one??? It's just two atoms (not including hydrogens) with a single bond between them or did I misunderstand the question completely? Igor On Thu, Mar 20, 2014 at 10:54 AM, scott_m js...@cam.ac.uk wrote: Hi all, I would like to generate conformers for molecules such as C2H6 and N2H4, is this possible? The bonds in these molecules are not being detected as rotatable bonds, why is this? Best wishes, Scott -- View this message in context: http://forums.openbabel.org/Conformer-searching-tp4657314.html Sent from the General discussion mailing list archive at Nabble.com. -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Conformer searching
They're the type of tools I'm looking for but they don't produce any conformers for N2H4 and C2H6. Thanks, Scott On 20 March 2014 15:49, Pascal Muller pascal.jm.mul...@gmail.com wrote: Hi, Thanks Igor but that was just an example of how you could find the minima from input structures, I am interested in generating the conformers using openbabel. What about http://openbabel.org/wiki/Obconformer for the command line tool or http://openbabel.org/dev-api/group__conformer.shtml if you want to customize. I didn't try it myself, though. Best regards, Pascal -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Two smi conversion problems
I originally used C=0 but using [C-]#[O+] gives the following roundtrip for me: [C-]#[O+] - SDF - [C-]#[OH] Since writing the above I tried installing the latest version of Open Babel and using C=0 now gives an error and using [C-]#[O+] gives the correct result. Thanks for the help with this, I think the new version has solved the problem. Best wishes, Scott On 13 March 2014 12:22, Geoffrey Hutchison geoff.hutchi...@gmail.comwrote: Thanks for the reply, the sdf file was actually produced from a smiles string using gen3d. OK, I guessed that, but what was the original SMILES? And what version of Open Babel are you using? The current development code roundtrips: [C-]#[O+] - SDF - [C-]#[O+] Thanks, -Geoff -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Two smi conversion problems
Thanks for the reply, the sdf file was actually produced from a smiles string using gen3d. Best wishes, Scott On 12 March 2014 22:05, Geoffrey Hutchison geoff.hutchi...@gmail.comwrote: 1. When converting a sdf file (see attached) for carbon monoxide to smi format I get the following smi result: [C-]#[OH] The SDF says it came through Open Babel.. presumably from some other format. It gives formal charges: M CHG 2 1 -1 2 1 This gives a -1 charge to the carbon and +1 to the oxygen: Certainly the SMILES has an issue (why it protonated the oxygen) -- the current development version gives: [C-]#[O+] But I'm guessing you'd like a better SMILES for carbon monoxide. OK, but the input is the issue. How/where did you get that SDF? 2. Hydrogens are inserted when converting the smiles P#P for the diphosphorus molecule to sdf format (see attached) using gen3d. Indeed, there's clearly an issue with the valence for triple-bonded phosphorous. There's no case for this in OB's atom typing, so it falls back to an implicit valence of 3 (i.e., one connection to the P plus 2 hydrogens). You can correct this by adding the following line to the atomtyp.txt file: IMPVAL [$([#15]#*)]1 # for P#P -Geoff inline: Screen Shot 2014-03-12 at 5.58.05 PM.png-- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Unable to set up forcefield for coordinates from mol file
Problem solved, many thanks for all the helpful replies! It was, as pointed out, a problem with the units. All the best, Scott On 9 October 2013 02:40, Geoffrey Hutchison geoff.hutchi...@gmail.comwrote: Indeed, Open Babel does support reading Dalton input files: obabel -L formats … dalmol -- DALTON Input So you can use -idalmol to specify the format as DALTON input format when reading. The unit conversion will happen automatically. Hope that helps, -Geoff -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60134071iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] UV-Vis inormation in .cml files
Hi Paolo, You can extract the excitation energies and oscillator strengths using CCLIBhttp://cclib.sourceforge.net/wiki/index.php/Main_Page. Uv-vis spectra can be created by fitting gaussian functions to the discrete plot of oscillator strengths and excitation energies. A paperhttp://pubs.acs.org/doi/full/10.1021/ct100662nby Caricato et al mentions simulated spectra obtained from the oscillator strengths by adding Gaussian line shapes through the Harada-Nakanishi equation. Hope this helps, Scott On 25 March 2013 17:06, paolo.posocco poso...@gmail.com wrote: Hi everybody! I'm an undergraduate italian student. I'm new in the field of computational chemistry. I would like to develop a UV-Vis spectra generator from Dalton output for my thesis. If i manage to use .cml filetype for input I could extent the script for a lot of QC softwares. I tried to convert a .log Gaussian output file containing UV-Vis information in *.cml using openbabel to understand the structure of this information but output doesn't contain any excitation energies and oscillator strengths. I ask you if this feature is implemented or not and if I could achieve this goal in another way. Thank you. -- View this message in context: http://forums.openbabel.org/UV-Vis-inormation-in-cml-files-tp4656102.html Sent from the General discussion mailing list archive at Nabble.com. -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion
Hi Chris, Thanks for your reply and apologies for the delayed response. Converting the cif to xyz and viewing the molecule shows the correct structure but converting the xyz file to smi and then generating coordinates and viewing shows the addition of a H atom. The correct smiles is: C(=O)(O)C[C@@H](C(=O)[O-])[N]1C=C[N+]=C1 The other smiles is:C(=O)([C@@H](CC(=O)O)N1C=CNC1)O One strange feature is that there doesn't appear to be a double bond between the N atom in the ring and the C atom, leaving the C atom with only three bonds. The smiles conversion seems to want to add a H here to get the correct bonding. Similarly for an ion, using smiles conversion results in the addition of H's. I've attached the cif file. Many thanks, Scott On 30 November 2012 14:53, Chris Morley c.mor...@gaseq.co.uk wrote: On 30/11/2012 12:03, scott_m wrote: Dear all, The conversion of (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate from a .cif file to .smi and subsequent generation of coordinates from the .smi file results in the addition of an extra H to one of the ring C atoms. The original cif formula is C7H8N2O4 but this changes to C7H9N2O4, which is no longer a zwitterion. I also noticed that converting an ion to smi and then from smi to xyz resulted in the addition of hydrogen atoms. Can this be avoided? Is the smi conversion of ions and zwitterions known to cause problems? Getting added hydrogens right is a recurrent issue. However the conversion from SMILES to xyz (and other formats) seems ok. Your problem may be in the conversion of the cif file, but you will need to append it for somebody (probably not me) to debug. obabel -:C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1 (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate -oxyz --gen3D --title --append formula 21 C7H8N2O4 C 2.456020.705701.56344 O 3.445920.485862.25208 O 1.436561.466702.00415 C 2.263560.114370.19030 C 3.145460.74947 -0.88078 H 2.848310.31396 -1.84634 C 2.830382.27406 -0.99631 O 1.670902.60592 -0.61087 O 3.794412.97728 -1.40748 N 4.601370.42805 -0.71225 C 5.359000.947620.25841 N 6.587890.461240.10334 H 7.339920.616600.75954 C 6.69161 -0.15933 -1.12882 C 5.43119 -0.14873 -1.66026 H 0.845361.765801.27272 H 1.204390.19509 -0.08254 H 2.46795 -0.957670.27113 H 5.047741.616431.05753 H 7.65241 -0.48371 -1.46628 H 5.01646 -0.45579 -2.60586 1 molecule converted Chris -- Keep yourself connected to Go Parallel: TUNE You got it built. Now make it sing. Tune shows you how. http://goparallel.sourceforge.net ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss SOXGES.search2.cif Description: Binary data -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion
Apologies, it was attached in the e-mail before last but had an identifier name (SOXGES.search2.cif) and so may have caused confusion. I've attached it again in this e-mail. As a general question, is it possible to convert coordinates to smiles that will always preserve the elements present (but may not get the bonding correct)? Best wishes, Scott On 4 December 2012 16:54, Chris Morley c.mor...@gaseq.co.uk wrote: Your problem is the incorrect conversion of a cif file, but you haven't shown one yet. (Not that I know much about cif files, but others may.) Conversions in OB go through an internal data structure, OBMol. It sound like the problem is in the cif to OBMol part, not in the OBMol to SMILES. Chris On 04/12/2012 15:34, Scott McKechnie wrote: Thanks Chris for the helpful comments. Sorry to keep on but I'm still left with the problem on going from cif to smiles where the original number of elements is not conserved. What I want is to be able to reliably represent the original cif molecule as a smiles string and from there recreate the molecule with gen3d. The problem at the moment is that the number of H atoms is changing. Any work around for this? On 4 December 2012 15:05, Chris Morley c.mor...@gaseq.co.uk mailto:c.mor...@gaseq.co.uk wrote: Scott Your correct smiles is not right. The sum of the bond orders to the charged nitrogen should be 4, and is only 3 (it has no H attached). The correct SMILES is in my post below. Even with it, the round trip via xyz: obabel -:C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1 -oxyz --gen3D | obabel -ixyz -osmi --append formula 1 molecule converted C(=O)(O)C[C@@H](C(=O)[O])N1CNC=C1 C7H8N2O4 1 molecule converted gives a di-radical rather than a zwitterion because xyz does not represent charges (or even bonds) and so OpenBabel didn't get any hints. xyz format is poor choice of format for general use. The round trip works ok with formats like mol or cml. Chris On 04/12/2012 10:51, Scott McKechnie wrote: Hi Chris, Thanks for your reply and apologies for the delayed response. Converting the cif to xyz and viewing the molecule shows the correct structure but converting the xyz file to smi and then generating coordinates and viewing shows the addition of a H atom. The correct smiles is: C(=O)(O)C[C@@H](C(=O)[O-])[N]1C=C[N+]=C1 The other smiles is:C(=O)([C@@H](CC(=O)O)N1C=CNC1)O One strange feature is that there doesn't appear to be a double bond between the N atom in the ring and the C atom, leaving the C atom with only three bonds. The smiles conversion seems to want to add a H here to get the correct bonding. Similarly for an ion, using smiles conversion results in the addition of H's. I've attached the cif file. Many thanks, Scott On 30 November 2012 14:53, Chris Morley c.mor...@gaseq.co.uk mailto:c.mor...@gaseq.co.uk mailto:c.mor...@gaseq.co.uk mailto:c.mor...@gaseq.co.uk wrote: On 30/11/2012 12:03, scott_m wrote: Dear all, The conversion of (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate from a .cif file to .smi and subsequent generation of coordinates from the .smi file results in the addition of an extra H to one of the ring C atoms. The original cif formula is C7H8N2O4 but this changes to C7H9N2O4, which is no longer a zwitterion. I also noticed that converting an ion to smi and then from smi to xyz resulted in the addition of hydrogen atoms. Can this be avoided? Is the smi conversion of ions and zwitterions known to cause problems? Getting added hydrogens right is a recurrent issue. However the conversion from SMILES to xyz (and other formats) seems ok. Your problem may be in the conversion of the cif file, but you will need to append it for somebody (probably not me) to debug. obabel -:C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1 (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate -oxyz --gen3D --title --append formula 21 C7H8N2O4 C 2.456020.705701.56344 O 3.445920.485862.25208 O 1.436561.466702.00415 C 2.263560.114370.19030 C 3.145460.74947 -0.88078 H
Re: [Open Babel] OBAlign() error
Excellent, working perfectly now, many thanks. I used your calcrmsd.py script from an earlier thread as a starting point for my scripts, so to avoid any future problems a simple canonical conversion of the conformers can be added in? This might be repetitive if done already but it would save any potential problems. Best wishes, Scott On 16 October 2012 16:40, Noel O'Boyle baoille...@gmail.com wrote: See the docs: When aligning molecules, the atoms of the two molecules must be in the same order for the results to be sensible. Try rearranging the atoms into canonical order first: obabel C:\Users\noel\Desktop\conf1.mol2 -O tmp.mol2 --canonical obabel C:\Users\noel\Desktop\conf2.mol2 -O tmp2.mol2 --canonical - Noel On 16 October 2012 16:23, scott_m js...@cam.ac.uk wrote: Dear all, I have been using OBAlign() to get rmsd values between conformers but just came across an erroneous value of 3.14 for the molecule N-Acryloyl glycine, the CSD function tormat gives a rmsd of 0 for the two conformers. Any idea what is going wrong here? I've attached the two mol2 files. Thanks, Scott conf1.mol2 http://forums.openbabel.org/file/n4655579/conf1.mol2 conf2.mol2 http://forums.openbabel.org/file/n4655579/conf2.mol2 -- View this message in context: http://forums.openbabel.org/OBAlign-error-tp4655579.html Sent from the General discussion mailing list archive at Nabble.com. -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Adding Hydrogens not working
Hi Noel, Many thanks for your answer which is exactly what I'm looking for. However, for some reason the hydrogens are still not being added when I use the command. I've attached the CIF file in case I have missed something. Thanks, Scott On 10 September 2012 22:46, Noel O'Boyle baoille...@gmail.com wrote: (Forgot to cc to the list) Hi Scott, The missing information is what bonds connect the heavy atoms as without this it's not possible to deduce where (and how many) the hydrogens are. But there should be no need to worry about this. Just use Open Babel to convert the cif file and add hydrogens: obabel myfile.cif -O myfile.xyz -h Behind the scenes, OB determines (i.e. wise guesses) the bond orders (i.e. single, double, etc.), and then -h tells it to add hydrogens. These are added in 3D space based on the coodinates of the neighbouring atoms. On 8 September 2012 18:01, scott_m js...@cam.ac.uk wrote: I have a problem with the following smiles [O][N][C]([C])[C] and related smiles. When I try to add hydrogens nothing happens. The correct formula is C3H7NO. It looks to be some problem with the square brackets but I don't know how to automatically adjust the smiles so that it will add the right amount of H's to match the chemical formula. Background: I have a number of CIF files and I want to extract the 3D coordinate information of the molecules but the H's are not always listed in the coordinate section (despite being in the formula). To fix this I was hoping to add hydrogens with openbabel. Thanks, Scott -- View this message in context: http://forums.openbabel.org/Adding-Hydrogens-not-working-tp4655446.html Sent from the General discussion mailing list archive at Nabble.com. -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ACEOXM.cif Description: Binary data -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Converting files with open babel
To whom it may concern, I am having problems when trying to convert files. I am trying to convert a .sdf file to a gaussian input file .com: babel opt.sdf opt.com babel: cannot write output format! Open Babel 2.3.1 -- May 1 2012 -- 16:34:16 Usage: babel [-iinput-type] name [-ooutput-type] name Try -H option for more information. I keep getting the above error and I have tried different files and different conversions, none seem to be working. I installed open babel today with the command: cmake ../openbabel-2.3.1 -DCMAKE_INSTALL_PREFIX=/scratch/jsm78/ -DBUILD_GUI=OFF make make install Some basic command results: which babel /scratch/jsm78/bin/babel babel -V Open Babel 2.3.1 -- May 1 2012 -- 16:34:16 System details: Distributor ID: SUSE LINUX Description:openSUSE 11.4 (x86_64) Release:11.4 Codename: Celadon Any help would be greatly appreciated. Best wishes, Scott -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
