[Open Babel] problem with --gen3D

I a trying to generate a 3D structure in directly from a smiles input as indicated in the manual. So for example, to generate the 3D structure of succinic acid, I am doing the following: echo "C(O)OCCC(O)O" > succinic.smi obabel -ismi succinic.smi -omol2 -O succinic.mol2 -h --gen3D however obab

Re: [Open Babel] Problem with gen3D keyword

The warnings are simply indicating that in the geometry optimization, the coordinates at that step were a bit rough and the gradient is high. They can be ignored. No, conformational search won't help here. -Geoff > Geoff, I'll try Avogadro, but my initial plan was to get the coordinates the >

Re: [Open Babel] Problem with gen3D keyword

>I get the xyz coordinates, but I also get a warning message: > WARNING: too small "scale" at Newton2NumLineSearch This is a minor warning from the geometry optimization. (Clearly I need to hide this.) > I need to grow the four alkyl chains of the structure. Why don't you create the methy

[Open Babel] Problem with gen3D keyword

Hi, I am trying to convert the following SMILES string (to xyz coordinates (with explicit hydrogens). [S@]1(C)[Au][S@]([Au][S@](C)[Au][S@]([Au]1)C)C I get the xyz coordinates, but I also get a warning message: WARNING: too small "scale" at Newton2NumLineSearch I need to grow the fo

Re: [Open Babel] Problem with --gen3D Open Babel 2.3.1

The problem is solved in the 2.3.2 release! Thank you very much. > I'm on trunk version and conversion is successful. > > [maciek@fokus ~]$ obabel > -:"OP(=O)(O)OC[C@H]1O[C@H]([C@@H]([C@@H]1O)OCC(=O)c1c2cc3c3cc2ccc1)n1cnc2c(=O)[nH]c(N)nc12" > -ismi -omol2 --gen3d > @MOLECULE > * > 65 70

Re: [Open Babel] Problem with --gen3D Open Babel 2.3.1

I'm on trunk version and conversion is successful. [maciek@fokus ~]$ obabel -:"OP(=O)(O)OC[C@H]1O[C@H]([C@@H]([C@@H]1O)OCC(=O)c1c2cc3c3cc2ccc1)n1cnc2c(=O)[nH]c(N)nc12" -ismi -omol2 --gen3d @MOLECULE * 65 70 0 0 0 SMALL GASTEIGER @ATOM 1 O 2.4378 -1.0815 -1.3719 O.3

Re: [Open Babel] Problem with --gen3D Open Babel 2.3.1

Have you tried it with OB 2.3.2? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/1/20 David García Aristegui > OK, is an open bug http://sourceforge.net/p/openbabel/bugs/833/ > > > Hello, i'm trying to assign 3D coordinates to this SMILES structure > > > > OP(=

Re: [Open Babel] Problem with --gen3D Open Babel 2.3.1

OK, in the News section of the Openbabel main page is announced "2011-10-17 Open Babel 2.3.1 Released only", i'm downloading the 2.3.2 release. I will try to do the conversion with the new release, but the bug is "Milestone: 2.3.x". By the way, would you be so kind to try to do the conversion, if

Re: [Open Babel] Problem with --gen3D Open Babel 2.3.1

OK, is an open bug http://sourceforge.net/p/openbabel/bugs/833/ > Hello, i'm trying to assign 3D coordinates to this SMILES structure > > OP(=O)(O)OC[C@H]1O[C@H]([C@@H]([C@@H]1O)OCC(=O)c1c2cc3c3cc2ccc1)n1cnc2c(=O)[nH]c(N)nc12 > > obabel is unable to resolve the structure > > time obabel --gen3

[Open Babel] Problem with --gen3D Open Babel 2.3.1

Hello, i'm trying to assign 3D coordinates to this SMILES structure OP(=O)(O)OC[C@H]1O[C@H]([C@@H]([C@@H]1O)OCC(=O)c1c2cc3c3cc2ccc1)n1cnc2c(=O)[nH]c(N)nc12 obabel is unable to resolve the structure time obabel --gen3D -ismi 3.3_30.smi -omol2 -O 3.3_30.mol2 1 molecule converted real6m8.1

Re: [Open Babel] Problem with gen3D

Thanks Geoff, I have some distance geometry code in python and I'm playing with that, but not all distance geometry implementations are of equal quality. I'm working with large numbers of small and medium sized molecules derived from messy crystallography data, so my main goal is a robust function

Re: [Open Babel] Problem with gen3D

> Thanks for the reply - this problem occurs in the builder.Build method > before the force field optimization, where initial coordinates are > given to each atom. It's not so much an issue of the "constraints" as the fact that you have a messy fused-ring system. The ring perception and particula

Re: [Open Babel] Problem with gen3D

Thanks for the reply - this problem occurs in the builder.Build method before the force field optimization, where initial coordinates are given to each atom. -Peter On Fri, Jul 20, 2012 at 8:02 AM, scott_m wrote: > Gen3d does a steepest descent optimization, weighted rotor search and then a > co

Re: [Open Babel] Problem with gen3D

Gen3d does a steepest descent optimization, weighted rotor search and then a conjugate gradients optimization (see http://forums.openbabel.org/what-does-gen3d-do-under-the-hood-td3397296.html). You might want to try a simple forcefield optimization to start with (like steepest descent) and see how

[Open Babel] Problem with gen3D

I've been having trouble with the 3D coordinate generation in Open Babel. The generator hangs on particular molecules with complicated bonding, and my guess is that the code gets stuck in an infinite loop when it can't satisfy all the constraints while building a 3D structure. For example the foll