I'd have to hunt through the code more carefully, but in formats like Gaussian,
we know that all atoms (including hydrogens) are explicit.
Unfortunately, that's not true from PDB — in the vast majority of cases,
hydrogens are omitted and implicit.
So, for example in src/formats/pdbformat.cpp
Den 2019-10-18 kl. 23:04, skrev Geoffrey Hutchison:
How about Gaussian log files? It works with those as well.
Somehow there bond orders are derived correctly as well although no such
information is extracted from the log files.
Are you saying that PDB is giving you different information than
> obenergy -ff GAFF file.pdb
> I get different bonds then when I run
> obenergy -ff GAFF file.sdf
>
> Since the atomtyping is done based on smarts I wonder whether different
> algorithms are used for generating smarts depending on the input file?
Different file types may or may not present full
Does your pdb file have hydrogens? If not, even more guessing. Gaussian
files have all the atoms at least.
On Fri, 18 Oct 2019, 19:54 David van der Spoel,
wrote:
> Den 2019-10-18 kl. 20:37, skrev Noel O'Boyle:
> > With pdb files we have to guess the bond orders. With sdf files, we
> > don't.
Den 2019-10-18 kl. 20:37, skrev Noel O'Boyle:
With pdb files we have to guess the bond orders. With sdf files, we
don't. There shouldn't be any other difference.
How about Gaussian log files? It works with those as well.
Somehow there bond orders are derived correctly as well although no such
With pdb files we have to guess the bond orders. With sdf files, we don't.
There shouldn't be any other difference.
On Fri, 18 Oct 2019, 18:52 David van der Spoel,
wrote:
> Hi,
>
> it seems that the algorithm for determining bonds and atomtypes depends
> on the input file, is that correct?
>
David,
have you tried to see if other bond-typed formats, like Mol2, give the same or
different
results?
I suspect the bond typing to play a role in this issue. In my experience with
SMARTS and
PDBs, I noticed that very often bond recognition failed, sometimes due to tiny
deviations
from
