Hi Michal,
Ouch, it looks like I have somehow forgotten about this. I’ll have a look next
week and get back to you.
Cheers,
p.
> On 10 Aug 2018, at 19:20, Michal Krompiec <michal.kromp...@gmail.com> wrote:
>
> 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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