AFAIK the only correlation is the molecule(s) you are "conformering" (is
that a verb?).
And no number of numConfs can be considered enough, let alone a number
of maxAttempts.
It depends on the problem you are wanting to solve, the molecules you
are looking at, and the amount of CPU you have to crack that particular nut.
I tend to use 1.5x - 2.0x but for a set of (fairly small) molecules.
If your molecules are more flexible then you maybe you need to go 10x.
Tim
On 17/12/2019 19:57, topgunhaides . wrote:
Hi Tim,
Many thanks for your help! One further question:
Is there any correlation between the maxAttempts and numConfs?
For instance, do I need to set a higher maxAttempts value if I request
a higher numConfs value?
Or to put it another way, what maxAttempts value can be considered as
"enough"?
Best,
Leon
On Tue, Dec 17, 2019 at 12:22 PM Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
This is in regard to the pruneRmsThresh option which removes very
similar conformers.
If let's say numConfs is set to 10 and maxAttempts is set to 20
then it will use UP TO 20 attempts to generate 10 conformers.
If too many conformers get rejected due to pruneRmsThresh then you
will end up with less than 10 conformers.
Or to put it another way, maxAttempts avoids you trying for ever
to generate conformers that are all the same and getting rejected!
Tim
On 17/12/2019 16:24, topgunhaides . wrote:
Hi guys,
Can anyone tell me more about the "maxAttempts" option in
"EmbedMultipleConfs"?
In the documentation, it says " maxAttempts: the maximum number
of attempts to try embedding".
Dose it mean the "maximum number of attempts" to generate each
conformer or to generate the total number of conformers
specified by "numConfs"? Or something else?
I need to generate a huge amount of conformers for each molecule,
so I want to know what is the proper "maxAttempts" to reach a
balance between accuracy and cost.
Thank you!
Best,
Leon
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