Hi all,
I'm looking at carbon bonded to benzene. The carbon can bond at all the
equivalent carbon in the benzene, as well as several other places in my
simulation.
I am trying to compare structures by their RMSD, to determine the unique
bonding structures. However, when I use OpenBabel the RMSD
rotate 60 degrees (360/6) around the ring. Perhaps, I’ll
try all 5 permutations and take the lowest RMSD as the correct RMSD .
Sent from Mail for Windows 10
From: Noel O'Boyle [via Open Babel]
Sent: Saturday, July 22, 2017 11:57 AM
To: CodyA
Subject: Re: Put atoms of target molecule in
A little late, but if anyone else has this problem.
Try running make install.
For some reason babel needs to be installed to work even though the CMake
tests will pass.
Without running make install no formats will be available as well, therefore
you shouldn't be able to convert file formats.
Hi I'm wondering if it anyone knows how to add hydrogen-bonding water to
molecules at specific sites. In addition, it would be useful to distinguish
whether the water is acting as a H-bond acceptor or H-bond donor.
There are several openbabel cpp functions that seem relevant, especially in
mcdlut
