I haven't tried it, but I'm assuming that once Paolo's pull request is
accepted, this will work out of the box.
https://github.com/rdkit/rdkit/pull/261
-David
On Fri, May 16, 2014 at 1:51 PM, Jan Domanski <jan...@gmail.com> wrote:
> The reply from Paolo was amazing and quick. I'm looking at this after a
> week and one questions comes to mind: Is there a reason this can't work out
> of the box?
>
>
> On 11 May 2014 23:08, Jan Domanski <jan...@gmail.com> wrote:
>
>> 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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>>>
>>>
>>> _______________________________________________
>>> Rdkit-discuss mailing
>>> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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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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