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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