Partial Charges in Avogadro

Hi everybody.

I’ d like to know which charges Avogadro displays when I choose " partial
charges " in label object. Why is not possible to show the partial
charges calculated by mopac or gamess

So, thank you everybody for your attention.

ps: is there any " course" or meeting to learn how to create (using
python) modules to avogadro ?

once again, thanks!

Fernando Bachega

On Aug 4, 2010, at 1:13 AM, José Fernando Ruggiero Bachega wrote:

I’ d like to know which charges Avogadro displays when I choose " partial charges " in label object. Why is not possible to show the partial charges calculated by mopac or gamess

By default, once you’ve imported a molecule, it will grab partial charges from MOPAC or GAMESS. You previously sent a MOPAC file, and it imported fine for me. What version of Avogadro are you using? What version of Open Babel?

ps: is there any " course" or meeting to learn how to create (using python) modules to avogadro ?

We’re definitely adding on to the wiki documentation:
http://avogadro.openmolecules.net/wiki/Category:Scripting

I think the best thing to do is to ask more questions, so we have an idea what kinds of examples we should add.

Thanks,
-Geoff

Hi Geoff, how are you?

As always, thanks for your attention!!!

I’ d like to know which charges Avogadro displays when I choose "
partial charges " in label object. Why is not possible to show the
partial charges calculated by mopac or gamess

By default, once you’ve imported a molecule, it will grab partial charges
from MOPAC or GAMESS. You previously sent a MOPAC file, and it imported fine
for me. What version of Avogadro are you using? What version of Open Babel?

My Avogadro is 1.0.0, and babel is 2.2.3. The charges calculated by
mopac and displayed by Gabedit are diferents than when I open the mopac
output file in Avogadro. Indeed, the charges displayed in Avogadro are
the same as if I draw the mocule in avogadro, without any QM proceeding.

ps: is there any " course" or meeting to learn how to create (using
python) modules to avogadro ?

We’re definitely adding on to the wiki documentation:
http://avogadro.openmolecules.net/wiki/Category:Scripting

I think the best thing to do is to ask more questions, so we have an idea
what kinds of examples we should add.

Thanks,
-Geoff

So, I have a suggestion, would be great to work with proteins in
avogadro, if like in pymol, select resides by reside name, in a list (sorry
if this option is already avalible in Avogadro).

So Thanks Geoff for your attention !

2010/8/4 Geoffrey Hutchison geoff.hutchison@gmail.com

On Aug 4, 2010, at 1:13 AM, José Fernando Ruggiero Bachega wrote:

I’ d like to know which charges Avogadro displays when I choose "
partial charges " in label object. Why is not possible to show the
partial charges calculated by mopac or gamess

By default, once you’ve imported a molecule, it will grab partial charges
from MOPAC or GAMESS. You previously sent a MOPAC file, and it imported fine
for me. What version of Avogadro are you using? What version of Open Babel?

ps: is there any " course" or meeting to learn how to create (using
python) modules to avogadro ?

We’re definitely adding on to the wiki documentation:
http://avogadro.openmolecules.net/wiki/Category:Scripting

I think the best thing to do is to ask more questions, so we have an idea
what kinds of examples we should add.

Thanks,
-Geoff


The Palm PDK Hot Apps Program offers developers who use the
Plug-In Development Kit to bring their C/C++ apps to Palm for a share
of $1 Million in cash or HP Products. Visit us here for more details:
http://p.sf.net/sfu/dev2dev-palm


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

My Avogadro is 1.0.0, and babel is 2.2.3. The charges calculated by mopac and displayed by Gabedit are diferents than when I open the mopac output file in Avogadro. Indeed, the charges displayed in Avogadro are the same as if I draw the mocule in avogadro, without any QM proceeding.

I can now reproduce this and will have a fix for the current development version of Open Babel. This will shortly be released as OB-2.3, but if you’re willing to compile from source code, I can send you a snapshot.

[Snip … need for more python examples and documentation]

So, I have a suggestion, would be great to work with proteins in avogadro, if like in pymol, select resides by reside name, in a list (sorry if this option is already avalible in Avogadro).

I think Tim would be the one to comment here. I know it’s possible to select residues by name in the user interface, but I do not know if this is possible in python.

Best regards,
-Geoff

On Mon, Aug 9, 2010 at 8:39 PM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

My Avogadro is 1.0.0, and babel is 2.2.3. The charges calculated by mopac and displayed by Gabedit are diferents than when I open the mopac output file in Avogadro. Indeed, the charges displayed in Avogadro are the same as if I draw the mocule in avogadro, without any QM proceeding.

I can now reproduce this and will have a fix for the current development version of Open Babel. This will shortly be released as OB-2.3, but if you’re willing to compile from source code, I can send you a snapshot.

[Snip … need for more python examples and documentation]

So, I have a suggestion, would be great to work with proteins in avogadro, if like in pymol, select resides by reside name, in a list (sorry if this option is already avalible in Avogadro).

I think Tim would be the one to comment here. I know it’s possible to select residues by name in the user interface, but I do not know if this is possible in python.

You could write tools to make it easier to work with proteins in
python. There is an example on the wiki with some protein related
function.

http://avogadro.openmolecules.net/wiki/Protein.py

This gives the following menu items: “Select Backbone”, “Select Side
Chains”, “Select Binding Site” and “Cut Surface”

The performance isn’t great though and I wanted to do much more
complex things so C++ seems the obvious choice.

I have some initial code for this actually. It is a very simple
scripting language (OBScript) and I mainly use it for working with
proteins. There are variables (no OO objects) and predefined
functions. Some examples

protein = read(“protein.pdb”)
backbone = select_backbone(protein)
residues = select_residues(protein, “10,13-15, D17-TYR24, ALA34-56”)
correct_protein(protein) # in progress, fixes missing atoms/bonds and so on
ff = get_forcefield(“UFF”)
fix_atoms(ff, backbone)
steepest_descent(ff, protein)
write(“protein_optimized_sidechains.pdb”)

It will not become a full scripting language but it is ideal for a
terminal. You can also add additional functions using a plugin
mechanism. For example, Avogadro could have a plugin with functions
that work directly on the molecule:

protein = read(“protein.pdb”)
avo_add_molecule(protein) # adds the molecule to the avogadro display
avo_select(protein) # makes a selection in avogadro
avo_deselect(protein)
avo_deselect() # deselect all
backbone = select_backone(protein) # obscript selection
avo_select(backbone) # use the obscript selection to select the
atoms/bonds in avogadro
avo_select_backone()
avo_select_residues(“11-23”)

I could also provide some overload method if this sounds to complicated.

All code is in a single file so it would be easy to embed this with
the avogadro code. It’s not complete since I mainly add functions as I
need them. However, I think something like this would make working
with proteins much easier.

Any suggestions on this? Any help would be welcome including making up
a list of functions there should be.

Best regards,
-Geoff