If you comment out the second azide expression in phmodel.txt all is
well. I've filed a bug. Maybe Chris can make sense of this.
- Noel
On 30 August 2012 12:48, Douglas Houston wrote:
> Thanks Paolo,
>
> Unfortunately the behaviour I described persists with SVN 4995.
>
> cheers,
>
> Doug
>
>
>
>
Thanks Paolo,
Unfortunately the behaviour I described persists with SVN 4995.
cheers,
Doug
Quoting Paolo Tosco on Thu, 30 Aug 2012 11:48:51 +0200:
> Dear Douglas,
>
> did you try to use the SVN version? I myself submitted a number of
> fixes to the pdbqt format module which might solve yo
Hi,
I don't know if this is related, but I've found another example of
what appears to be an "erroneous structure" with the -p option in
2.3.1. I noticed it when converting to PDBQT format, but there's also
a problem when I convert to PDB. The files in question are attached.
babel -isdf i
Just following up on this as Chris just fixed the issue reported by
Douglas. The problem in your case is different, if it is actually an
error by Open Babel. If you look in phmodel.txt, you can see all of
the protonation rules. The one being applied in your case is:
#guanidine or amidine
TRANSFORM
Hey Douglas, thank you for your help and for the information provided. I'll
take this into account.
I hope somebody could fix this bug soon. The '-p' option seems so useful to
me.
Cheers!
--
View this message in context:
http://forums.openbabel.org/erroneous-structures-when-the-option-p-is-act
This may be related to a longstanding bug that has yet to be fixed. See:
http://sourceforge.net/tracker/index.php?func=detail&aid=3203137&group_id=40728&atid=428740
This essentially makes the -p option unusable if you are expecting
charges in the output format.
Quoting green69 on Fri, 15 Ju
Hi guys!
I'm using Open Babel 2.3.1 in a GNU/Linux (2.6.32-5-amd64) machine with
debian OS.
openbabel generate erroneous structures when the option "-p" to add
hydrogens appropriate for a certain pH is activated and the output is SMILES
or canonical SMILES. An example is provided with 3 files:
http
