Dear Rafal,

answers below.

On 10/14/16 13:53, Rafal Roszak wrote:
> Dear all,
>
> 1. I want to generate gromacs topology with force field parameters
> from SMILES. RDKit has two FFs so this should be easy task at least for
> this two force fields. Bond and angle parameters can be simply take
> from Get*BondStretchParams and Get*StretchBendParams, but vdW and
> torsian parameters are not so obvious.
> -) How to assign vdW params to atoms? How can I extract this from rdkit?
The RDKit currently returns has two Get*VdWParams() functions which 
retrieve the vdW parameters for a specific *pair* of atoms, i.e. after 
the {MMFF, UFF} combination rules have been applied. I can add getters 
for the raw per-atom vdW parameters; I'll let you know once they are 
implemented.
> -) How to convert result of Get*TorsionParams (Inversion and OopBend) to
> something which can be used by gromacs? (I know, it is not strictly
> question about RDKit)
I am not myself a Gromacs user and I don't know about the Gromacs 
topology format, so I am afraid I can't help with this one.
>
> 2. It think I found bug in MMFF implementation:
>
>>>> acetona=Chem.AddHs(Chem.MolFromSmiles('[CH2-]C(=O)C') )
>>>> AllChem.MMFFHasAllMoleculeParams(acetona)
> True
>>>> acetmm=AllChem.MMFFGetMoleculeProperties(acetona)
>>>> sumch=0
>>>> for i in range( len(acetona.GetAtoms()) ):
> ...  sumch+=acetmm.GetMMFFPartialCharge(i)
> ...
>>>> round(sumch,2)
> 0.0
>>>> for i in range( len(acetona.GetAtoms()) ):
> ...  sumch+=acetmm.GetMMFFFormalCharge(i)
> ...
>>>> round(sumch,2)
> 0.0
>
> The molecule is anion but sum of formal or partial charge is zero. In
> my opinion it is not currect result :) The same behaviour I also
> observed for other exotic C-anion.
>
The MMFF force field does not have parameters for carbanions nor for 
carbocations, so AllChem.MMFFHasAllMoleculeParams() should return False. 
Thanks for reporting this; I'll file a bug and fix it as soon as I have 
a bit of time.

Best,
Paolo
> Regards,
>
> RafaƂ
>
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