Avogadro question

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.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_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!

Hello David, how do you do?

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.

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: loniedavid@gmail.com
Date: Tue, 24 Jan 2012 10:05:09 -0500
Subject: Re: avogadro question
To: davidea86_30@hotmail.com
CC: avogadro-discuss@lists.sourceforge.net

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.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_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!

On Wed, Jan 25, 2012 at 5:02 PM, David Velasco Villamizar
davidea86_30@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: loniedavid@gmail.com
Date: Tue, 24 Jan 2012 10:05:09 -0500

Subject: Re: avogadro question
To: davidea86_30@hotmail.com
CC: avogadro-discuss@lists.sourceforge.net

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.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_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!

I’m using Avogadro 1.03 under ubuntu linux. I think I’ve learned how to do conformational searching (using
mmff94) and can review the list of structures and energies it finds. It seems that last structure (lowest energy?)
is displayed when the search is done, and this is THE one saved when save file is used. However, what I’d like
to do is save (all? certain selected?) structures and their energies in a single output file that I could use as a
source of initial structures for subsequent work. Is there a way to do this? The xyz format would be handy, with
the MM energy in the text label line for a multiple structure file.
Thanks,
Steve Williams

source of initial structures for subsequent work. Is there a way to do this? The xyz format would be handy, with
the MM energy in the text label line for a multiple structure file.

Yes, a few people have asked for this feature, but it’s not implemented yet. I’ll add it to my ToDo list, since a colleague here is bugging me about it too.

-Geoff


Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

Thanks, Geoff.
Steve

----- Original Message -----
From: Geoffrey Hutchison geoff.hutchison@gmail.com
Date: Sunday, January 29, 2012 4:14 pm
Subject: Re: [Avogadro-Discuss] save conformational search
To: avogadro-discuss@lists.sourceforge.net

source of initial structures for subsequent work. Is there a way
to do this? The xyz format would be handy, with
the MM energy in the text label line for a multiple structure file.

Yes, a few people have asked for this feature, but it’s not
implemented yet. I’ll add it to my ToDo list, since a colleague
here is bugging me about it too.

-Geoff


Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/



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Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss

Perhaps Avogadro generates a file with a specific atoms parameter that it uses to optimize with MMFF94.

Avogadro determines the MMFF94 atom types internally (i.e., in memory) and does not write it to a file.

If you want to define atom types, such as for MMFF94, you should look at the Open Babel “Tinker” file format:
http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html

Hope that helps,
-Geoff