On 12/19/19 7:27 PM, Francois Berenger wrote:
>
> You should parallelize the processing of molecules, since each can be
> worked at independently.
>
Well, for "a lot" of conformers on "a lot" of molecules that'll work if
you have access to a compute cluster and/or are willing to pay for
Hi Rafal,
Thank you for this suggestion. I will try these to see the changes.
Best,
Leon
On Thu, Dec 19, 2019 at 4:37 AM Rafal Roszak wrote:
> On Wed, 18 Dec 2019 22:54:04 -0500
> "topgunhaides ." wrote:
>
> > For large and flexiable molecules, will need a lot more than 10K (like
> > 100K)
Hi Michal,
Many thanks for the help!
The MMFF will be mainly used to remove only the (very) high energy
conformers, which is a good news here.
There is one dilemma here:
Without optimization, some potentially "good" conformers could be
filted out, due to the fact that small unreasonable atomic
Hi Greg,
Many thanks for the help!
The main purpose that I am "trying to generate a huge number of conformers
for a bunch of molecules" is to reproduce experimentally determined
structures.
To increase accuracy, I want to try the following at least:
- cover the entire (not quite possible for
For mid-to-lower-energy conformers, MMFF relative energies are
essentially a fancy random-number generator. Still, all depends on
what you need this for. If you just want to filter out (very) high
energy conformers, your approach might work. But if you also want to
perform Boltzmann averaging over
On Wed, 18 Dec 2019 22:54:04 -0500
"topgunhaides ." wrote:
> For large and flexiable molecules, will need a lot more than 10K (like
> 100K) to try to cover the entire conformational space.
In such case
useExpTorsionAnglePrefs=True,
useBasicKnowledge=True
can make your conformational set less
Hi Leon,
If you want to be able to work efficiently on a problem like this, it's
important to first take a step back and think about what you're doing.
In this particular case you are asking the RDKit to generate 1
conformers for a molecule and requiring that the RMSD between each of those
Hi Michal,
Many thanks for the help! I am looking for an ensemble of conformers.
My priority is to use RDKit to generate a large ensemble of conformers for
each molecule.
For large and flexiable molecules, will need a lot more than 10K (like
100K) to try to cover the entire conformational space.
Are you looking for the global minimum or an ensemble of conformers? Either
way, this is already very fast. Bear in mind, however, that MMFF’s accuracy
isn’t great for this type of tasks (see for example
https://arxiv.org/pdf/1705.04308.pdf ). In other words, I don’t see a use
case for generation
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