Awesome, this was lightning speed Paolo - many thanks!
- Jan
On 10 May 2014 20:47, Paolo Tosco <paolo.to...@unito.it> wrote:
> Dear Jan,
>
> the reason why your restraint was seemingly not applied is that
> MMFFAddTorsionConstraint() expected a range such as (170, 190). I have just
> modified the code to make it more robust in this respect and I submitted a
> pull request to Greg. Meanwhile, you may get the results you expect using a
> (170, 190) degree range.
> Please find attached a slightly modified version of your python script; in
> particular, I added a call to SetDihedralDeg() before the constrained
> minimization, to avoid troubles to the minimizer in case the geometry
> generated by EmbedMultipleConfs() has dihedral values very far from the
> desired target value.
>
> Thanks for your detailed report which allowed chasing down that weakness
> in my code!
>
> Cheers,
> Paolo
>
>
> On 05/10/2014 04:28 PM, Jan Domanski wrote:
>
> Hi there,
>
> Attached is a crystal_ligand.mol2 for the ACE target from DUDE. I'd like
> to generate a number of conformers for this ligand. The trick is it has 2
> amide bonds that I'd like to keep planar. As far as I can see neither MMFF
> nor UFF will keep those planar by default, at least not for this input
> file.
>
> One way around it, is to find all the amide bonds by smarts matching.
> From that, find the hydrogen connected to N and add a DihedralConstraint on
> the 4 atoms before running the minimization.
>
> That's what conformers.py is attempting to do (basing on one of the test
> scripts). However, I still get non-planar amide bonds and I'm really
> confused as to why. I can filter them out manually with GetDihedralDeg().
>
> Thanks for all the help (I'm using up all the rdkit credits this weekend
> ;) )
>
> - Jan
>
>
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> --
> ==========================================================
> Paolo Tosco, Ph.D.
> Department of Drug Science and Technology
> Via Pietro Giuria, 9 - 10125 Torino (Italy)
> Tel: +39 011 670 7680 | Mob: +39 348 5537206
> Fax: +39 011 670 7687 | E-mail: paolo.tosco@unito.ithttp://open3dqsar.org |
> http://open3dalign.org
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