On Wed, Jan 25, 2012 at 5:02 PM, David Velasco Villamizar <davidea86...@hotmail.com> wrote: > I'm so sorry another time to bother you with my question, but right now I > guess that my last message ending up in misunderstanding. Let's me tell > you, my main interest with Advogadro is making molecules and try to > optimizing them at the same time, but I do not really know one way to make > molecular dynamics using Advogadro, so for that reason I have been working > with other program called, GROMACS, which in it, I have to introduce a > document with the information of all parameter about atoms (bonds, angles, > torsion, van der Waals,etc ) beside the file.pdb (molecule). > > According with the link http://openbabel.org/wiki/OBForceFieldMMFF94 that > you kindly sent me, I want to know which are the constant that Avogadro uses > to make the optimization, I mean, the constant related with MMFF94 this > force field, how it identify which one is which one????? If I can get > this kind of information, I will can transform the formulas of MMFF94 and > the constant to other Force Field from then OPLS library.
Ah, so you are looking for the parametrization constants of the force fields. The definitive source for these will be the papers describing the methods, which are given on the wiki pages I sent earlier. The actual values used in Avogadro come from the OpenBabel implementations of the forcefields. The files that contain the parameters can be found in the trunk/data/ subdirectory of the openbabel source code: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk/data/ For instance, the UFF parameters are here: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk/data/UFF.prm The MMFF94 parameters are spread out across several .par files, e.g. torsions are defined in: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk/data/mmfftor.par But these parameter files are rather cryptic, and reading the papers describing the methods should provide a much clearer understanding of the parameters and how they are used. I am not aware of any method in Avogadro or OpenBabel that prints out the parameters used for a specific molecule -- you will need to read the papers or decipher the raw parameter files/OpenBabel source code to find them. Dave > Perhaps Avogadro generates a file with a specific atoms parameter that it > uses to optimize with MMFF94. > > Let's me be more exactly, how can I get the parameter of the MMFF94 > corresponding to the adjunct molecule??? To make the optimization? > > > Thanks so much, I will be absolutely grateful with your answer. > > > >> From: lonieda...@gmail.com >> Date: Tue, 24 Jan 2012 10:05:09 -0500 > >> Subject: Re: avogadro question >> To: davidea86...@hotmail.com >> CC: avogadro-discuss@lists.sourceforge.net > >> >> Hi David, >> >> On Mon, Jan 23, 2012 at 4:56 PM, David Velasco Villamizar >> <davidea86...@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: lonieda...@gmail.com >> >> Date: Mon, 23 Jan 2012 14:36:36 -0500 >> >> Subject: Re: avogadro question >> >> To: davidea86...@hotmail.com >> >> >> >> Hi 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/OBForceFieldUFF >> >> >> >> If 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...@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! >> >> > ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! 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