Hi David,
On Mon, Jan 23, 2012 at 4:56 PM, David Velasco Villamizar
davidea86_30@hotmail.com wrote:
Let’s me tell you that your answer was absolutely useful to my research and
it helped me to have a new landscape of Avogadro Program, but right now I’m
totally interested to find a way in Avogadro to generate a file or and
option where I can get the information related with the atomic parameter
that it used to make the optimization(the parameter of the Force Field and
what kind of atom are evolving), I mean, is there a way to generate from
Avogadro a topology file of the molecule over a determined force field?
I’ve cc’d this email to the avogadro discussion mailing list, someone
there may be more familiar with what you need.
I’m not sure what you mean by a “topology file”, and how it would
relate to the forcefield? Could you provide an example of what such a
file would contain?
You’ve mentioned bond properties (angles, torsions, etc) – perhaps
the “report” format would provide what you are looking for. Open your
molecule in Avogadro and select “File > Save as”. Save it with a
“.report” extension, e.g. “c60-opt.report”. This will produce a text
file that contains a distance matrix, bond angles, and torsion angles.
See the attached for an example. There are many more formats that can
be used that may be useful, like the “gzmat” format which produces a
zmatrix. A full list of supported extensions and their descriptions is
here:
http://openbabel.org/docs/dev/FileFormats/Overview.html
If you’re on linux, you can also perform these conversions on the
command line with the “babel” command:
babel -i[input extension] [inputfile] -o[output extension] [outputfile]
So for the pdb file you sent,
babel -ipdb c60-opt.pdb -oreport c60-opt.report
will produce the c60-opt.report file.
Dave
From: loniedavid@gmail.com
Date: Mon, 23 Jan 2012 14:36:36 -0500
Subject: Re: avogadro question
To: davidea86_30@hotmail.comHi David,
The energy minimization / geometry optimization feature in Avogadro
uses a molecular mechanics forcefield to evaluate the energy of the
molecule and search for locally optimal geometries. Depending on which
forcefield is used (Avogadro supports several; GAFF, Ghemical, MMFF94,
UFF…), the formulas and parameters used in the energy calculations
are linked to or provided on the OpenBabel wiki:http://openbabel.org/wiki/Molecular_mechanics
http://openbabel.org/wiki/OBForceFieldGhemical
http://openbabel.org/wiki/OBForceFieldMMFF94
http://openbabel.org/wiki/OBForceFieldUFFIf you just want to measure the optimized bond lengths, angles,
torsions, etc, the “Measure” tool will help with this. The Avogadro
wiki provides more information on the use of the tool:http://avogadro.openmolecules.net/wiki/Category:Tools
Hope this helps,
Dave
On Mon, Jan 23, 2012 at 6:50 AM, David Velasco Villamizar
davidea86_30@hotmail.com wrote:Hello David, how do you do?
Let’s me ask you something, but first of all a little introduce of
myself,
I’m David Velasco V. I have been working in my research project in the
Institute of Physics, University of Santa Catarina, Brazil. Actually
I’ve
been present some problems related with some calculation of molecules,
more
exactly P3HT/C60, which my interest is to get a right energy
optimization
(geometry with minimum of energy) but I haven’t got a right idea about
the
atoms’ parameter that Avogadro uses to do it, that means, what is the
length
of bounding? angles between atoms? and torsion angles between four
atoms?
partial charge? If I can subtract this kind of information from the
Avogadro’s program, I will can do my next steep rightly in molecular
dynamics with other program and use it to organic solar cells research.Let’s me know you answer,
Before hand, thanks so much!
David!