Hi Thomas,
I had a similar problem, but in my case checking for unusually long bonds
(e.g. longer than typical bond length times an experimental multiplier) and
"additional" close contacts, i.e. more close contacts (excluding h-bonds)
between atoms separated by at least 4 bonds (if I remember correctly) than
in a conformer without restraints did the trick. You may also want to tweak
the force constant of the restraints.
Kind regards,
Michal

On Thu, 23 Feb 2017 at 13:50, Thomas Evangelidis <teva...@gmail.com> wrote:

> Greetings,
>
> I want to create conformations of molecules using restraints but many of
> the resulting conformers have wrong geometries (distorted aromatic, rings,
> out-of-plane hydrogens, etc.). I would like to define some rules of thump
> to recognize such wrong geometries. One possible way is to look at the
> total energy of the molecules as given by
> AllChem.UFFGetMoleculeForceField.CalcEnergy(). However, the energy
> threshold is different for every molecule. Therefore I thought to define an
> arbitrary threshold dependent on the total number of heavy atoms, like N*20
> kcal/mol. When all the generated conformers exceed that energy thresholds,
> then more conformers are generated until I get at least one with valid
> energy. I would like to know your opinion on this matter. What would be a
> reasonable multiplier (in my example I used 20 kcal/mol)? Would you
> recommend adding other factors (e.g. number of rotatable bonds) in my
> empirical rule to exclude wrong geometries?
>
> Another way could be to apply bond and dihedral angle constrains to the
> aromatic atoms based on their configuration in the starting conformation
> (which has always correct geometry). But that would be more tedious than
> the energy threshold approach. Do you think that this is the right way to
> go?
>
> Thanks in advance.
> Thomas
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> Research Specialist
> CEITEC - Central European Institute of Technology
> Masaryk University
> Kamenice 5/A35/1S081,
> 62500 Brno, Czech Republic
>
> email: tev...@pharm.uoa.gr
>
>           teva...@gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
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