[Rdkit-discuss] position restraints on all atoms

[Katrina Lexa]

Hi All,

I'm relatively new to RDKit, so I apologize for what may be a silly
question. I'd like to generate a set of local minimum conformations around
my input conformation, using a set of defined flat bottom potentials (0.2,
0.6, 1.0, and 1.4), in order to better compare my bound conformation with
its unrestrained minimum.

Ultimately, I'd like to write a script that reads in one input 3D
conformation and prints out the energy and rmsd (and structure) of those
local minimums as well as the lowest energy unrestrained conformation.

There are plenty of examples of conformer generation scripts for RDKit, but
I'm struggling with the constraints piece. I see the MMFFFixedAtoms &
MMFFPositionConstraints code, but based on the code it's not obvious to me
whether it's possible to implement either as a constraint on all atoms in
my input molecule. Is there a way or is there another route I should be
taking?

Thanks for the help,

Katrina

[Francois BERENGER]

Post by Katrina Lexa
Hi All,
I'm relatively new to RDKit, so I apologize for what may be a silly
question. I'd like to generate a set of local minimum conformations
around my input conformation, using a set of defined flat bottom
potentials (0.2, 0.6, 1.0, and 1.4), in order to better compare my bound
conformation with its unrestrained minimum.
Ultimately, I'd like to write a script that reads in one input 3D
conformation and prints out the energy and rmsd (and structure) of those
local minimums as well as the lowest energy unrestrained conformation.
There are plenty of examples of conformer generation scripts for RDKit,
but I'm struggling with the constraints piece. I see the MMFFFixedAtoms
& MMFFPositionConstraints code, but based on the code it's not obvious
to me whether it's possible to implement either as a constraint on all
atoms in my input molecule. Is there a way or is there another route I
should be taking?

Maybe this can give you some inspiration:

"3D diverse conformers generation using rdkit"
https://github.com/UnixJunkie/smi2sdf3d

Post by Katrina Lexa
Thanks for the help,
Katrina
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[Greg Landrum]

Hi Katrina,

welcome to the RDKit community!

Post by Katrina Lexa
I'm relatively new to RDKit, so I apologize for what may be a silly
question. I'd like to generate a set of local minimum conformations around
my input conformation, using a set of defined flat bottom potentials (0.2,
0.6, 1.0, and 1.4), in order to better compare my bound conformation with
its unrestrained minimum.
Ultimately, I'd like to write a script that reads in one input 3D
conformation and prints out the energy and rmsd (and structure) of those
local minimums as well as the lowest energy unrestrained conformation.
There are plenty of examples of conformer generation scripts for RDKit,
but I'm struggling with the constraints piece. I see the MMFFFixedAtoms &
MMFFPositionConstraints code, but based on the code it's not obvious to me
whether it's possible to implement either as a constraint on all atoms in
my input molecule. Is there a way or is there another route I should be
taking?

Apologies for asking what may be an obvious clarification question, but
what are you planning on constraining? It sounds like you want to attach
"springs" (well, flat bottom potentials) between the atoms in your
generated conformations and the corresponding atoms in a reference
conformation and calculate the energy of that system. Is that right?

If so, you can do this by generating a force field for the molecule with
your generated conformations, adding fixed points corresponding to your
reference conformation, and then adding distance contraints with the
appropriate min (I guess 0) and max values and reasonable force constants.
Subtracting the energy of the generated conformation from the energy of
this full system gives you the energy contributed by the constraints.

I can provide a bit of sample code showing how to do this, but I want to be
sure that this is actually what you're asking for.

-greg

[Francois BERENGER]

Hello,

Is it possible to decompose partial charges with rdkit?

I am afraid that Gasteiger-Marsili (PEOE) is mostly about sigma bonds,
but I might be wrong.

Regards,
F.