>> + if (atom->IsNitrogen() && atom->GetFormalCharge() == 0 &&
>> atom->GetValence() == 3 && charge > 0) {
>> +atomState[idx] = DOUBLE_ALLOWED; // It has an electron it can
>> donate, because of the total charge
>> + charge--;
>> +if (DEBUG) { cout << "atom " << i
On 2014-03-08 22:21, Paul van Maaren wrote:
> I had a look at it too, the following hack seems to work for all types
> of imidazolium ions.
>
> In gaussformat.cpp I moved mol.SetTotalCharge(charge) close to the
> location where the charge is extracted from the Gaussian file and in
> kekulize.cpp I
I had a look at it too, the following hack seems to work for all types
of imidazolium ions.
In gaussformat.cpp I moved mol.SetTotalCharge(charge) close to the
location where the charge is extracted from the Gaussian file and in
kekulize.cpp I added the following:
diff --git a/src/kekulize.cpp b/s
> 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
