Re: [Open Babel] Prevent addition of H during minimization
Hi Hetal, As I always comment, "OB is not adding hydrogens. The hydrogens are already there, just implicit." That is, your original MOL file is in fact Li(OH)2 (but you can't tell that unless you are familiar with the MOL file spec). How are you creating the input file? Is there a way to set the valence? You need to set the valence for the oxygens to force them to valence 1 (Roman capital I), otherwise there's an implicit H. Otherwise, just manually edit the file so that it looks something like: 3 2 0 0 0 0 0 0 0 0999 V2000 0.0.0. Li 0 0 0 0 0 0 0 0 0 0 0 0 0.0.0. O 0 0 0 0 0 1 0 0 0 0 0 0 0.0.0. O 0 0 0 0 0 1 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 1 0 0 0 0 M END Regards, Noel On Fri, 31 Mar 2023 at 15:43, Hetal Patel wrote: > Hi, > > I am trying to use minimization feature using uff but it is adding > hydrogens to fill the shell. How do I prevent from addition of any > additional atoms beyond what is in the input file. > > Here is a same input and the command I am using. > > Input.mol > > > > > 3 2 0 0 0 0 0 0 0 0999 V2000 > 0. -0. -0. Li 0 0 0 0 0 0 0 0 0 0 0 0 > 0.4622 -0.2286 -0.0600 O0 0 0 0 0 0 0 0 0 0 0 0 >-0.44340.21930.0576 O0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 0 0 0 > 1 3 1 0 0 0 0 > M END > > Command: obabel input.mol -O output.mol --minimize --steps 1 --sd --ff > uff > > > output.mol: > > > OpenBabel03302314253D > > 5 4 0 0 0 0 0 0 0 0999 V2000 >-0.0207 -0.0375 -0.0870 Li 0 0 0 0 0 0 0 0 0 0 0 0 > 1.7549 -0.3412 -0.5469 O 0 0 0 0 0 0 0 0 0 0 0 0 >-1.79570.26680.3744 O 0 0 0 0 0 0 0 0 0 0 0 0 > 2.27200.23590.0697 H 0 0 0 0 0 0 0 0 0 0 0 0 >-1.78700.32811.3627 H 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 0 0 0 > 1 3 1 0 0 0 0 > 2 4 1 0 0 0 0 > 3 5 1 0 0 0 0 > M END > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Helps me
Hello. I'm a doctoral student and I'm using openbabel for my thesis. Currently, I want to prepare a ligand for my molecular docking. For this, I take the ligand in SMILES format and converted it to SDF or MOL format. With scripts of the tutorial: PROMPT> obabel -ismi 'outputfile.smi' -osdf 'mymols.sdf' As a result, I have an error and I'm not understood why == *** Open Babel Error in OpenAndSetFormat Cannot open /home/virginia/Escritorio/Doctorado/LideB/Ácido == *** Open Babel Error in OpenAndSetFormat Cannot open Zolendrónico/SMILE == *** Open Babel Error in OpenAndSetFormat Cannot open /home/virginia/Escritorio/Doctorado/LideB/Ácido == *** Open Babel Error in OpenAndSetFormat Cannot open Zolendrónico/SDF 0 molecules converted I hope that somebody helps me. Thank's Virginia. ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Prevent addition of H during minimization
Hi, I am trying to use minimization feature using uff but it is adding hydrogens to fill the shell. How do I prevent from addition of any additional atoms beyond what is in the input file. Here is a same input and the command I am using. Input.mol 3 2 0 0 0 0 0 0 0 0999 V2000 0. -0. -0. Li 0 0 0 0 0 0 0 0 0 0 0 0 0.4622 -0.2286 -0.0600 O0 0 0 0 0 0 0 0 0 0 0 0 -0.44340.21930.0576 O0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 1 0 0 0 0 M END Command: obabel input.mol -O output.mol --minimize --steps 1 --sd --ff uff output.mol: OpenBabel03302314253D 5 4 0 0 0 0 0 0 0 0999 V2000 -0.0207 -0.0375 -0.0870 Li 0 0 0 0 0 0 0 0 0 0 0 0 1.7549 -0.3412 -0.5469 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.79570.26680.3744 O 0 0 0 0 0 0 0 0 0 0 0 0 2.27200.23590.0697 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.78700.32811.3627 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 1 0 0 0 0 2 4 1 0 0 0 0 3 5 1 0 0 0 0 M END___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
