[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.

Re: [Open Babel] obminimize outputs only in pdb (multimolecule pdb)

Hi Geoff, When I tried to convert a multimolecule pdb file (output from obminimize) to an sdf file, only the first molecule was converted. I wrote my own script to split the file into multiple pdbs and put them together as single sdf using obabel. But any solution using obabel to that in single

Re: [Open Babel] obminimize outputs only in pdb (multimolecule pdb)

Thanks. I will try that. Sundar Thangapandian > On Oct 19, 2017, at 6:40 PM, Geoffrey Hutchison > wrote: > > The obminimize program does not have all the features of the obabel command. > You can naturally convert a PDB file to SDF: > > obabel file.pdb -O file.sdf

Re: [Open Babel] obminimize outputs only in pdb (multimolecule pdb)

The obminimize program does not have all the features of the obabel command. You can naturally convert a PDB file to SDF: obabel file.pdb -O file.sdf > I tried -osdf filename.sdf and it didn't work. How can I get it in sdf format? > Or how can I convert multimolecule pdb file to an sdf file?

[Open Babel] obminimize outputs only in pdb (multimolecule pdb)

Hi, obminimize outputs only in pdb format. I tried -osdf filename.sdf and it didn't work. How can I get it in sdf format? Or how can I convert multimolecule pdb file to an sdf file? Thanks, Sundar -- Check out the

[Open Babel] Obminimize

Hi Noel, I tried to minimize ligands using obminimize when using earlier versions of obminimize after converged the output file will be redirected to a pdb file format. But when I tried using obminimize of openbabel version 2.4.0 even after convergence it performs minimization till the completion

Re: [Open Babel] obminimize

> If i use: obminimize [-ff forcield] [-algorithm] to calculate the > minimized energy of a given ligand a don't always get the same results. (of > course I only compare results with the same ligande, same forcefield and same > algorithm with each other) I'm not quite sure I understand what

[Open Babel] obminimize

Hello Guys Currently I'm writing my Bachelorthesis and therefor I'm using Openbabel for some calculations. Now i have the following problems. If i use: obminimize [-ff forcield] [-algorithm] to calculate the minimized energy of a given ligand a don't always get the same results. (of

Re: [Open Babel] obminimize

Thank you guys for your answer. I tried what you said but the output is not a sdf file. How to format it in order to obtain normal sdf file? alchemist -- Everyone hates slow websites. So do we. Make your web apps

Re: [Open Babel] obminimize

How stupid I am! Thanks Fredrik, that fix the problem. So thanks anyone for helping me. alchemist Оригинално писмо От: Fredrik Wallner fred...@wallner.nu Относно: Re: [Open Babel] obminimize До: Оги Боги Изпратено на: Четвъртък, 2013, Февруари 28 14:59:46 EET

Re: [Open Babel] obminimize

Try: obminimize -ff MMFF94 -sd source.sdf target.sdf Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/2/27 Оги Боги alchemist...@abv.bg Hi guys, I am trying to use obminimize under 64bit windows 7 in order to minimize geometry of molecules inside

[Open Babel] obminimize

Hi guys, I am trying to use obminimize under 64bit windows 7 in order to minimize geometry of molecules inside multimolecule sdf file. I'm using the following command: obminimize -ff MMFF94 -sd The problem is that obminimize prints results from minimization procedure in console but nothing

Re: [Open Babel] obminimize

On Feb 18, 2011, at 11:43 AM, christophersw...@btconnect.com wrote: Is it possible to get the obminimize tool to output anything other than pdb file format? Yes. Supply a '-o[ext]' flag. This works with v2.2 or later. Come to think of it, *you* asked for the feature! :-) Cheers, -Geoff

Re: [Open Babel] obminimize

Great after a few attempts I see what my problem was:- If I try the sort of construction used for other babel commands ChrisMacbookPro:~ swain$ /usr/local/bin/obminimize -ff -ff Ghemical -cg -n 2500 -c 1.0E-5 -cut -rvdw6.0 -rele 10.0 -pf 10 '/Users/swain/Desktop/output.sdf' -osdf

Re: [Open Babel] Obminimize

Could anyone help me to get energy minimal value for more than 2 decimal places, i need atleast 5 decimal places. For example I highly doubt the molecular mechanics energies have more than 2-3 decimal places of accuracy in either the model or implementation. (Yes, the