On 03/06/14 16:12, James Davidson wrote:
Dear All (but mainly Paulo!),
I have really been appreciating the MMFF implementation in RDKit --
particularly now with the ability to add position / distance / angle /
torsional constraints!
Dear James,
nice to hear that! This is the kind of comments that makes my day : )
I have a couple of naïve questions; and apologise in advance if I have
missed answers to these in the documentation / method doc-strings...
1. This is a simple one -- but just to categorically confirm --
ff.CalcEnergy() gives results in kcal/mol units, right?
Correct.
1. Now onto force constants... I see from the unittest (aka
documentation if you can't find anything else)
'testConstraints.py' that the value of 1.0e5 is used in the
tests. 1.0e5 what? And should this be viewed as a strong,
modest, or weak restraint? Presuming this constant is somewhat
like saying how springy a spring is(?), then what is a sensible
value to give me a super-strong steel joist that would essentially
resist everything (or is 1.0e5 it)?
Units of force constants for distance/position restraints are in kcal
mol^-1 ang^-2, while for angle/torsional constraints units are kcal
mol^-1 rad^-2. 1.0e5 is definitely a very stiff constraint. Milder
constraints would be in the range of 1 to 5, medium constraints in the
range of 10 to 100. However, it is a bit difficult to define how stiff a
constraint is in absolute terms, since it depends on the environment. If
with your constraint you are trying to lock a portion of the molecule in
a position which raises a bad van der Waals contact, for instance, it
could be that you have to use an even larger force constant since you
have to fight against a large energy term. In such a case, the
competition between large energy terms may result in distorted
geometries (you have surely seen this before when, for instance, trying
to minimize a ligand in a protein cavity stiffened with position
constraints, and the cavity is just not large enough for that ligand).
1. Final thing: the problem with making something really good /
useful is that people get used to it and then start wanting more!
How's the GBSA implicit solvation coming on? : )
Aw, here you are touching a painful chord in my heart. I would *love* to
implement GBSA in the RDKit (as well as other thingies), but I am afraid
this is not going to happen in the near future - I am not an academic
anymore, so time for playing with the RDKit has shrunk dramatically.
Kind regards
James
Kind regards,
Paolo
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