On Sat, Feb 15, 2014 at 02:22:27AM -0800, anna wrote:
Dear all,
I need to calculate electrostatic potential (ESP) derived atomic charges. I
did geometry optimization with MMFF94s force field. Is it also important to
do rotor search in order to minimize the molecule?
Usually an ensamble of
On Thu, Nov 21, 2013 at 06:26:14AM -0800, Rajesh wrote:
Thanks James and Dimitri for your quick reply.
As such I dont have any more versions installed in my machine other than the
2.3.2 source compiled version.
However, to be more precise on the issue, I have recompiled one more time,
On Thu, Jun 20, 2013 at 07:57:38PM -0700, Suraj Mirpuri wrote:
Thanks! I think I can take it from here, but a few more questions, as I
looked at the OBFit source and I am pretty confused on how it works. Isn't
there a superimpose method? What is the benefit to qtrfit? Also how do I
use these
On Wed, Feb 13, 2013 at 10:25:45AM -0500, Geoffrey Hutchison wrote:
I am trying to generate multiple conformation of small molecules. As a first
step I am trying to minimize the molecule.
However when I try to select the forcefield using
OBForceField* pFF =
On Sun, Oct 28, 2012 at 02:14:13PM +0100, David van der Spoel wrote:
Hi,
I'm trying to link my project to the development version of openbabel2
which is installed in $HOME/openbabel-dev/install
I there added the FindOpenBabel2.cmake that floats around the internet
to my software packages
On Wed, Oct 17, 2012 at 11:04:55AM +0200, Fredrik Wallner wrote:
If you build up the molecule from within OpenBabel, chances
are that that molecule will be possible to describe as a
SMILES string which is valid SMARTS.
This, and also look at the thread [OpenBabel-scripting] text
On Wed, Oct 17, 2012 at 06:24:06PM +0200, KC soh wrote:
Hi
I'm using Mac 10.6 and i tried to install the perl and python bindings but
i ran into this problem. I copied the Eigen folder into /usr/local/include
XXXmac2:build kc$ cmake ../openbabel-2.3.1 -DPYTHON_BINDINGS=ON
On Wed, Oct 17, 2012 at 09:36:40PM +0200, David van der Spoel wrote:
How can I contribute a feature to extract the G2 etc. Energies?
There is a patch tracker [1], you can post it there I think that
is the most appropriate. We are in process to migrate to Git, so
after that also git
On Wed, Oct 10, 2012 at 07:42:45PM +0200, David van der Spoel wrote:
At the very least that would eliminate any inconsistencies
between Gromacs and Open Babel generated files. I have
implemented GRO format support and OB can read XTC format, so
maybe TRR support is the only one really
On Wed, Oct 10, 2012 at 10:41:52AM +0200, David van der Spoel wrote:
On 2012-10-10 10:30, Noel O'Boyle wrote:
What is the link between Gaussian files and Gromacs? Or is this a
separate issue? I would have thought that Gromacs has the complete
structure with bond orders and explicit
On Tue, Oct 09, 2012 at 09:01:08AM +0200, David van der Spoel wrote:
On 2012-10-08 21:08, Reinis Danne wrote:
On Mon, Oct 08, 2012 at 07:40:51PM +0200, David van der Spoel wrote:
On 2012-10-08 19:11, Reinis Danne wrote:
On Mon, Oct 08, 2012 at 03:00:30PM +0200, David van der Spoel wrote
On Mon, Oct 08, 2012 at 10:55:12AM +0200, David van der Spoel wrote:
Hi,
sorry to be a pain but I found another few pathetic cases (chemistry has
a lot of them). Azulene C10H8 is a merged 5 and 7 ring, purely CH:
% babel -ipdb azulene.pdb -oinchi ---errorlevel
On Mon, Oct 08, 2012 at 07:40:51PM +0200, David van der Spoel wrote:
On 2012-10-08 19:11, Reinis Danne wrote:
On Mon, Oct 08, 2012 at 03:00:30PM +0200, David van der Spoel wrote:
It adds TWO H for InChi output, not for SDF output, but it only produces
two double bonds (out of three). I
On Sun, Oct 07, 2012 at 11:20:16AM +0200, David van der Spoel wrote:
Hi,
when reading a gaussian output file the total charge is available and
that could be used to improve the bond order perception, alternatively
there could be a command line option to tell babel about the total charge.
On Sun, Oct 07, 2012 at 08:32:53PM +0200, David van der Spoel wrote:
On 2012-10-07 18:35, Reinis Danne wrote:
On Sun, Oct 07, 2012 at 11:20:16AM +0200, David van der Spoel wrote:
Hi,
when reading a gaussian output file the total charge is available and
that could be used to improve
On Sat, Oct 06, 2012 at 01:06:51PM +0200, David van der Spoel wrote:
Hi,
I'm trying to implement an algorithm to determine bond orders into the
GROMACS MD package, and looked at the open babel version. There seems to
be a problem in the implementation however. If I convert the structure
On Wed, Oct 03, 2012 at 01:03:09PM -0700, Joaquin Peralta wrote:
Hello,
I did a plugin for openbabel, and check some examples that work fine. What
do I have to do to include this in the repositories, just submit using
subversion? Do I have to send to someone to test the plugin?
Probably the
17 matches
Mail list logo
