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 wrote: > Hi, > > > > > > Thanks Igor but that was just an example of how you could find the minima >> from input structures, I am interested i

Re: [Open Babel] Conformer searching

quantum > chemistry. > > Regards, > Igor > > > On Thu, Mar 20, 2014 at 11:15 AM, Scott McKechnie wrote: > >> Ethane (C2H6) and hydrazine (N2H4) have distinct minima that are >> separated by rotational barriers. Depending on the input structure, a >> geom

Re: [Open Babel] Conformer searching

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 wishe

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

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 wrote: > 1. When converting a sdf file (see attached) for carbon monoxide to smi > format I get the following smi result: > > [C-]#[OH] > > >

Re: [Open Babel] Smiles for diphosphorus

Hi Craig, Thanks for the reply. I used sdf: obabel -:'P#P' -osdf > P2.sdf --gen3d Best wishes, Scott On 8 November 2013 15:17, Craig James wrote: > On Fri, Nov 8, 2013 at 3:52 AM, scott_m wrote: > >> Hi all, >> >> When I use gen3d with P#P I get a molecule with two hydrogens. Should it >>

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 wrote: > Indeed, Open Babel does support reading Dalton input files: > > obabel -L formats > … > dalmol -- DALTON Input > >

Re: [Open Babel] UV-Vis inormation in .cml files

Hi Paolo, You can extract the excitation energies and oscillator strengths using CCLIB. Uv-vis spectra can be created by fitting gaussian functions to the discrete plot of oscillator strengths and excitation energies. A paper

Re: [Open Babel] Indexing in OBmol and OBMolAtomIter

Problem solved, many thanks. I was confused by the similarity of the names! On 15 March 2013 11:20, Noel O'Boyle wrote: > You have (understandably) confused two different things. atom.GetIdx() > is the function you were looking for, not GetIndex(). > > I don't understand the question about OBMol

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

gh 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 wit

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

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 > w

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@

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 po

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 wrote: > (For

[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 [-i] [-o] Try -H option for more inform