> Any pointers to where to start fixing this?
>
> I'm happy to do some programming, but it seems the problems lie deeper
> in the code than in forcefieldgaff.cpp.
>
>
Ive had a look at this - I think the problem is in the gaussian input parsing
the primary issue is that the SMILES from gaussi
On 2014-03-07 22:16, Geoffrey Hutchison wrote:
> I'm sorry, it's been a very hectic few weeks and I have not had much time for
> e-mail, much less coding.
>
No worries, that's life.
> As you suspect the problem is not with GAFF or SMARTS but the aromatic
> detection and Kekulization of the molecu
I'm sorry, it's been a very hectic few weeks and I have not had much time for
e-mail, much less coding.
As you suspect the problem is not with GAFF or SMARTS but the aromatic
detection and Kekulization of the molecules.
I'm not 100% certain where the problem is. The first question is this.. you
On 2014-03-05 22:30, David van der Spoel wrote:
> Dear list,
>
> we're struggling with getting OB to produce the right gaff atom parameters.
>
> We start from a Gaussian log file
> (http://folding.bmc.uu.se/1-ethyl-3-methylimidazolium3-esp.log.gz).
> Then, using
>
> obabel -ig09 1-ethyl-3-methylimi
