Dear Noel Thank you for your answer. Please see my comments bellow.
2017-05-22 16:00 GMT-03:00 Noel O'Boyle :
> In other words, you want to assign atom types based on the structure.
>
Yes, that's right.
> The source of the structure is immaterial except in so far as it
> introduces noise. F
Thank you Miro for your answer. Tha is in the spirit of we want to do, but
without writing an intermediate file. We think that all the conversions can
be done inside the code.
Marcos.
2017-05-22 16:06 GMT-03:00 Miro Moman :
> Quick and dirty workaround: Convert it to .xyz (removing the Hs if nee
Maybe if you can give an example of the problem with aromaticity, we
can help? The only information that is used by that function is the
structure, so it was probably wrong at that point.
On 23 May 2017 at 13:16, Marcos Villarreal wrote:
>
> Dear Noel Thank you for your answer. Please see my comm
When I convert the molecules as given with obabel, you're right - you
run into a bug that's been fixed on the development branch -
aromaticity is perceived differently depending on the presence/absence
of explicit hydrogens:
> obabel 3rlb_ligand.* -osmi
Cc1nc(N)c(Cn2csc(CCO)c2C)cn13rlb_ligand
Thank you Noel for look into this.
So how do you suggest to do this inside the code, that is without passing
for and intermediate file.
I remind you that our gol is to get the same atom types (say aromatics)
regardless the input format.
For now we are interested in consistency before "accuracy", w
> For now we are interested in consistency before "accuracy", which is another
> subject. As a related note, we have tested several atom typing programs
> (Knodle, I-interpret, Unicon and also Open Babel) and the perception of the
> number of aromatic atoms typically differ in 10-20 % when analy
Hello Geoff, thank you for your answer. Please see my comments which are
inline with yours comments below
2017-05-23 12:38 GMT-03:00 Geoffrey Hutchison :
> > For now we are interested in consistency before "accuracy", which is
> another subject. As a related note, we have tested several atom typi
On 05/23/2017 12:24 PM, Marcos Villarreal wrote:
> I agree with you in principle, but consider the following not uncommon
> scenario. We are working on docking (autodock vina) whose score depends on
> atom typing. As you know the ligands come in different formats, usually
> pdb, mol2 or sdf. We w
