Hi Paolo,
Thanks so much for your quick response.
Hmm… would you mind sharing how you are calculating those RMSDs? I’m seeing
RMSDs with constraints of over 1.0 Angstrom, so clearly some detail is
still escaping me.
My goal here is to reproduce the strain energy calculations that are part
of
Hi Paolo,
Thanks so much for this suggestion (ages ago now). Based on Francois’
suggestion and your suggestion I have cobbled together a script that seems
like it ought to work to apply position constraints on each atom, minimize,
and then return the local minima conformations. Perhaps I’m still
Hi Katrina,
you may add multiple constraints, of the same (e.g., positional) or
different kinds. Each of them will result in an additional force field
contribution being added to your system. So you may, for example,
identify a group that you wish to constrain by a SMARTS pattern,
identify
Thanks Greg!
Thanks Francois for your response.
Where I’m struggling is with generating locally restrained conformations.
Essentially, my question is about this line of code:
ff.MMFFAddPositionConstraint(1, 0.3, 1.0e5)
My reading of the code page is that the first variable, 1, describes which
Hi Katrina,
welcome to the RDKit community!
On Mon, Jul 24, 2017 at 10:45 PM, Katrina Lexa wrote:
>
> 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
On 07/25/2017 05:45 AM, Katrina Lexa wrote:
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
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