Re: [Rdkit-discuss] Restraining torsions whilst generating conformers
Hi Taka, I've been playing with the UFFAddTorsionConstraint suggestion but I can't make it work for my systems (although it is great to know about as I can think of lots of other uses). The problem is that the Embedded geometries are too far from the geometry that I want to enforce on the torsions so that if I actually apply a large enough force constant to get the desired torsions I blow up the molecule and if I reduce the force constant the torsions don't go anywhere near where I need them. I think that for now I might just go with some other conformer generator like Balloon, generate a silly number conformers and filter them for 'reasonable' ones using RDKit and go from there. Not ideal, but better than throwing my computer out the window because I can't get the RDKit embedding to do what I want :D Thanks for you suggestions. I know they'll come in handy for other things. Cheers, Bruce On Sun, 26 Apr 2020 at 13:28, Taka Seri wrote: > Hi Bruce, > > Thanks for your reply. > I searched rdkit documents and found that RDKit has some constraint method. > https://www.rdkit.org/docs/source/rdkit.ForceField.rdForceField.html > And I tried to use UFFAddTorsionConstraint for an example. > https://gist.github.com/iwatobipen/42c325f2471166ff4084051381d0ef78 > By using these method I think you can keep the torsions. > Thanks. > > Taka > > 2020年4月26日(日) 19:35 Bruce Milne : > >> Hi Taka, >> >> Thanks for the suggestion. The ConstrainedEmbed method is certainly >> useful but I need to only freeze some selected torsions and allow the rest >> of the macrocycle to remain flexible. If this was only a single part of the >> macrocycle the ConstrainedEmbed method would work but I need to >> simultaneously restrain several parts of the ring that are connected by >> flexible regions. >> >> Cheers, >> Bruce >> >> On Sun, 26 Apr 2020 at 02:00, Taka Seri wrote: >> >>> Dear Bruce, >>> >>> How about to use the defined core which has your desired torsions? >>> Here are examples to generate restricted conformers with user defined >>> cores. >>> >>> https://www.discngine.com/blog/2019/6/6/tethered-minimization-of-small-molecules-with-rdkit-towards-tethered-docking-on-proteins-with-rdock >>> http://rdkit.blogspot.com/2019/01/more-on-constrained-embedding.html >>> Thanks, >>> >>> Taka >>> >>> >>> >>> 2020年4月26日(日) 1:11 Bruce Milne : >>> Hi, Is it possible to add torsional restraints whilst using AllChem.EmbedMultipleConfs() to generate conformers? I did look at this some time back but ended up moving on to another project and never found out if it could be done. I asked a similar thing in this group at the time (about avoiding the generation of cis-peptide bonds) but I don't think it got an answer. I suspect that it may not be possible with AllChem.EmbedMultipleConfs() but if anyone knows of an alternative for generating partially constrained structures it would be good to know. Cheers, Bruce -- Prof. Dr. Bruce F. Milne CFisUC Department of Physics University of Coimbra Rua Larga 3004 - 516 Coimbra Portugal https://orcid.org/-0002-5522-4808 https://publons.com/researcher/2905148/bruce-milne/ https://www.linkedin.com/in/brucemilne A/h = S/k ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >> >> -- >> Prof. Dr. Bruce F. Milne >> CFisUC >> Department of Physics >> University of Coimbra >> Rua Larga >> 3004 - 516 Coimbra >> Portugal >> >> https://orcid.org/-0002-5522-4808 >> https://publons.com/researcher/2905148/bruce-milne/ >> https://www.linkedin.com/in/brucemilne >> >> A/h = S/k >> > -- Prof. Dr. Bruce F. Milne CFisUC Department of Physics University of Coimbra Rua Larga 3004 - 516 Coimbra Portugal https://orcid.org/-0002-5522-4808 https://publons.com/researcher/2905148/bruce-milne/ https://www.linkedin.com/in/brucemilne A/h = S/k ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Restraining torsions whilst generating conformers
Hi Bruce, Thanks for your reply. I searched rdkit documents and found that RDKit has some constraint method. https://www.rdkit.org/docs/source/rdkit.ForceField.rdForceField.html And I tried to use UFFAddTorsionConstraint for an example. https://gist.github.com/iwatobipen/42c325f2471166ff4084051381d0ef78 By using these method I think you can keep the torsions. Thanks. Taka 2020年4月26日(日) 19:35 Bruce Milne : > Hi Taka, > > Thanks for the suggestion. The ConstrainedEmbed method is certainly useful > but I need to only freeze some selected torsions and allow the rest of the > macrocycle to remain flexible. If this was only a single part of the > macrocycle the ConstrainedEmbed method would work but I need to > simultaneously restrain several parts of the ring that are connected by > flexible regions. > > Cheers, > Bruce > > On Sun, 26 Apr 2020 at 02:00, Taka Seri wrote: > >> Dear Bruce, >> >> How about to use the defined core which has your desired torsions? >> Here are examples to generate restricted conformers with user defined >> cores. >> >> https://www.discngine.com/blog/2019/6/6/tethered-minimization-of-small-molecules-with-rdkit-towards-tethered-docking-on-proteins-with-rdock >> http://rdkit.blogspot.com/2019/01/more-on-constrained-embedding.html >> Thanks, >> >> Taka >> >> >> >> 2020年4月26日(日) 1:11 Bruce Milne : >> >>> Hi, >>> >>> Is it possible to add torsional restraints whilst >>> using AllChem.EmbedMultipleConfs() to generate conformers? I did look at >>> this some time back but ended up moving on to another project and never >>> found out if it could be done. I asked a similar thing in this group at the >>> time (about avoiding the generation of cis-peptide bonds) but I don't think >>> it got an answer. >>> >>> I suspect that it may not be possible with AllChem.EmbedMultipleConfs() >>> but if anyone knows of an alternative for generating partially constrained >>> structures it would be good to know. >>> >>> Cheers, >>> Bruce >>> >>> -- >>> Prof. Dr. Bruce F. Milne >>> CFisUC >>> Department of Physics >>> University of Coimbra >>> Rua Larga >>> 3004 - 516 Coimbra >>> Portugal >>> >>> https://orcid.org/-0002-5522-4808 >>> https://publons.com/researcher/2905148/bruce-milne/ >>> https://www.linkedin.com/in/brucemilne >>> >>> A/h = S/k >>> ___ >>> Rdkit-discuss mailing list >>> Rdkit-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >> > > -- > Prof. Dr. Bruce F. Milne > CFisUC > Department of Physics > University of Coimbra > Rua Larga > 3004 - 516 Coimbra > Portugal > > https://orcid.org/-0002-5522-4808 > https://publons.com/researcher/2905148/bruce-milne/ > https://www.linkedin.com/in/brucemilne > > A/h = S/k > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Restraining torsions whilst generating conformers
Hi Taka, Thanks for the suggestion. The ConstrainedEmbed method is certainly useful but I need to only freeze some selected torsions and allow the rest of the macrocycle to remain flexible. If this was only a single part of the macrocycle the ConstrainedEmbed method would work but I need to simultaneously restrain several parts of the ring that are connected by flexible regions. Cheers, Bruce On Sun, 26 Apr 2020 at 02:00, Taka Seri wrote: > Dear Bruce, > > How about to use the defined core which has your desired torsions? > Here are examples to generate restricted conformers with user defined > cores. > > https://www.discngine.com/blog/2019/6/6/tethered-minimization-of-small-molecules-with-rdkit-towards-tethered-docking-on-proteins-with-rdock > http://rdkit.blogspot.com/2019/01/more-on-constrained-embedding.html > Thanks, > > Taka > > > > 2020年4月26日(日) 1:11 Bruce Milne : > >> Hi, >> >> Is it possible to add torsional restraints whilst >> using AllChem.EmbedMultipleConfs() to generate conformers? I did look at >> this some time back but ended up moving on to another project and never >> found out if it could be done. I asked a similar thing in this group at the >> time (about avoiding the generation of cis-peptide bonds) but I don't think >> it got an answer. >> >> I suspect that it may not be possible with AllChem.EmbedMultipleConfs() >> but if anyone knows of an alternative for generating partially constrained >> structures it would be good to know. >> >> Cheers, >> Bruce >> >> -- >> Prof. Dr. Bruce F. Milne >> CFisUC >> Department of Physics >> University of Coimbra >> Rua Larga >> 3004 - 516 Coimbra >> Portugal >> >> https://orcid.org/-0002-5522-4808 >> https://publons.com/researcher/2905148/bruce-milne/ >> https://www.linkedin.com/in/brucemilne >> >> A/h = S/k >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > -- Prof. Dr. Bruce F. Milne CFisUC Department of Physics University of Coimbra Rua Larga 3004 - 516 Coimbra Portugal https://orcid.org/-0002-5522-4808 https://publons.com/researcher/2905148/bruce-milne/ https://www.linkedin.com/in/brucemilne A/h = S/k ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Restraining torsions whilst generating conformers
Dear Bruce, How about to use the defined core which has your desired torsions? Here are examples to generate restricted conformers with user defined cores. https://www.discngine.com/blog/2019/6/6/tethered-minimization-of-small-molecules-with-rdkit-towards-tethered-docking-on-proteins-with-rdock http://rdkit.blogspot.com/2019/01/more-on-constrained-embedding.html Thanks, Taka 2020年4月26日(日) 1:11 Bruce Milne : > Hi, > > Is it possible to add torsional restraints whilst > using AllChem.EmbedMultipleConfs() to generate conformers? I did look at > this some time back but ended up moving on to another project and never > found out if it could be done. I asked a similar thing in this group at the > time (about avoiding the generation of cis-peptide bonds) but I don't think > it got an answer. > > I suspect that it may not be possible with AllChem.EmbedMultipleConfs() > but if anyone knows of an alternative for generating partially constrained > structures it would be good to know. > > Cheers, > Bruce > > -- > Prof. Dr. Bruce F. Milne > CFisUC > Department of Physics > University of Coimbra > Rua Larga > 3004 - 516 Coimbra > Portugal > > https://orcid.org/-0002-5522-4808 > https://publons.com/researcher/2905148/bruce-milne/ > https://www.linkedin.com/in/brucemilne > > A/h = S/k > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Restraining torsions whilst generating conformers
Hi, Is it possible to add torsional restraints whilst using AllChem.EmbedMultipleConfs() to generate conformers? I did look at this some time back but ended up moving on to another project and never found out if it could be done. I asked a similar thing in this group at the time (about avoiding the generation of cis-peptide bonds) but I don't think it got an answer. I suspect that it may not be possible with AllChem.EmbedMultipleConfs() but if anyone knows of an alternative for generating partially constrained structures it would be good to know. Cheers, Bruce -- Prof. Dr. Bruce F. Milne CFisUC Department of Physics University of Coimbra Rua Larga 3004 - 516 Coimbra Portugal https://orcid.org/-0002-5522-4808 https://publons.com/researcher/2905148/bruce-milne/ https://www.linkedin.com/in/brucemilne A/h = S/k ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
