Hi Paolo,
Has anything changed (re adding new atom types to UFF or MMFF) since then?
Best,
Michal
On Tue, 5 Nov 2013 at 06:56, Paolo Tosco <paolo.to...@unito.it> wrote:
> Hi both,
>
> now I realize that yesterday I replied to Michal and not to the list;
> sorry about that. Adding the option to force an atom type replacement
> wouldn't be too much work, but would not be ideal because in cause of
> selenium you would get, for instance, the same VdW radius and equilibrium
> bond distances as for sulfur, which would both be too short. That could
> also be handled upstream the atom typing by replacing Se with S and putting
> back Se downstream as I suggested yesterday to Michal, but again a bit of a
> hack. Probably a better solution would be to allow the user to provide some
> new parameters (as for UFF, adding Python support) and fall back to a
> related atom type (sulfur, in this case) for the missing ones. I'll look
> into that during the next days and let you know.
>
> Best,
> p.
>
> --
> ==========================================================
> Paolo Tosco, Ph.D.
> Department of Drug Science and Technology
> Via Pietro Giuria, 9 - 10125 Torino (Italy)
> Tel: +39 011 670 7680 | Mob: +39 348 5537206
> Fax: +39 011 670 7687 | E-mail: paolo.to...@unito.it
> http://open3dqsar.org | http://open3dalign.org
> ==========================================================
>
>
>
> On 5 Nov 2013, at 07:20, Greg Landrum <greg.land...@gmail.com> wrote:
>
> Hi Michal,
>
>
> On Mon, Nov 4, 2013 at 11:45 AM, Michal Krompiec <
> michal.kromp...@gmail.com> wrote:
>
>> Hello,
>> Is Se defined in UFF and/or MMFF94? Apparently, molecules with
>> selenophene moieties don't optimize in RDKit, and a warning appears in
>> the log: UFFTYPER: Unrecognized atom type: Se2+2
>>
>
> Right. UFF Parameters are there for sp3 Se ("Se3+2"), but not for the sp2
> version.
>
> There are no MMFF94 parameters for Se.
>
> Is it possible to define/modify the force field by hand? (for example,
>> use the parametrs of S for Se)
>>
>
> If you are working from C++, you can provide UFF parameters when you build
> the force field, but it's not currently possible to do so from Python. It's
> probably possible to add an option to the python UFF code to allow you to
> provide a new atom type (or to over-ride parameters for an existing atom
> type); I'd have to look into that.
> In the meantime, the quickest thing you could do would be to modify
> $RDBASE/Code/ForceField/UFF/Params.cpp to add the atom type you want and
> then to rebuild the RDKit.
>
> I guess that adding new atom types to MMFF94S is considerably more
> complex. Here one could imagine providing an interface to explicitly set
> the type of an atom to another existing atom type. Paolo would have to let
> us know how much work that is.
>
> -greg
>
>
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