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 <bfmi...@gmail.com>: > 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 <serit...@gmail.com> 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 <bfmi...@gmail.com>: >> >>> 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/0000-0002-5522-4808 >>> 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/0000-0002-5522-4808 > https://publons.com/researcher/2905148/bruce-milne/ > https://www.linkedin.com/in/brucemilne > > A/h = S/k >
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