What's up with Avogadro and PCGAMES/Firefly?

General Discussion
1

Hi people.

I saw a brief conversation about Avogadro and PCGAMES/Firefly, but no
conclusion… I 'm trying to open output files from firefly 7.1.G with
Avogadro, but no way, doesn’t work. Any suggestions ? Thks a lot
everybody !

bye

2

Hello.

I saw a brief conversation about Avogadro and PCGAMES/Firefly, but no
conclusion… I 'm trying to open output files from firefly 7.1.G with
Avogadro, but no way, doesn’t work. Any suggestions ? Thks a lot
everybody !

That’s strange. I 've just opened my output from this version. Maybe you
should rename your file to output.gamout so Avogadro would recognize format.

2010/5/13 José Fernando Ruggiero Bachega ferbachega@gmail.com

Hi people.

I saw a brief conversation about Avogadro and PCGAMES/Firefly, but no
conclusion… I 'm trying to open output files from firefly 7.1.G with
Avogadro, but no way, doesn’t work. Any suggestions ? Thks a lot
everybody !

bye

3

Hi there !

2010/5/13 Denis Lyubimov lyubimov.denis@gmail.com

Hello.

I saw a brief conversation about Avogadro and PCGAMES/Firefly, but no
conclusion… I 'm trying to open output files from firefly 7.1.G with
Avogadro, but no way, doesn’t work. Any suggestions ? Thks a lot
everybody !

That’s strange. I 've just opened my output from this version. Maybe you
should rename your file to output.gamout so Avogadro would recognize format.

I did, and now I can see the molecule, but no molecular orbitals yet and
no electrostatic surface too.

Any other tip?

Thks a lot for your attention

best regards

4

Hello again.

Sorry I can’t check following instruction with Avogadro right now.

But if you want firefly to output information about orbitals for MacMolPlot
you must provide MOLPLT=.TRUE.
option within your $CONTRL group. Something like this.

$CONTRL SCFTYP=RHF RUNTYP=HESSIAN MOLPLT=.TRUE. $END

However there are two problems.

  1. I don’t know if Avogadro could parse that data at all.

  2. Firefly slightly changed output format for that data (changed header
    string for this data section in output file), and now MacMolPlot could not
    parse these files. This is known problem,as you can see official US GAMESS
    webpage. So Avogadro may be affected too, even if it could parse usual
    GAMESS US files.

Unfortunately I haven’t enough time and skills now to contribute tweaks for
this to Avogadro code. And not even couple months from now. But it must be
relatively simple, and if there is a bug/feature you could request it. I am
sorry I can’t do more than writing this letter.

Denis.

////////////////////////////////////////////////////////////////////////////
2010/5/13 José Fernando Ruggiero Bachega ferbachega@gmail.com

Hi there !

2010/5/13 Denis Lyubimov lyubimov.denis@gmail.com

Hello.

I saw a brief conversation about Avogadro and PCGAMES/Firefly, but no
conclusion… I 'm trying to open output files from firefly 7.1.G with
Avogadro, but no way, doesn’t work. Any suggestions ? Thks a lot
everybody !

That’s strange. I 've just opened my output from this version. Maybe you
should rename your file to output.gamout so Avogadro would recognize format.

I did, and now I can see the molecule, but no molecular orbitals yet and
no electrostatic surface too.

Any other tip?

Thks a lot for your attention

best regards

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Avogadro-Discuss@lists.sourceforge.net
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5
  1. I don’t know if Avogadro could parse that data at all.

Avogadro does not yet parse GAMESS or MacMolPlt orbital data. If someone would like to send me some example files, I can take a crack at it.

Best regards,
-Geoff

6

Hello.

Sorry I messed up. Firefly outputs in MacMolPlot files only coordinates, so
there is no need to play with it, and even more it outputs in PUNCH not,
*.gamout file

Here you can get zip file with two input,gamout and PUNCH files for
semi-empirical PM3 and ab initio 6-31G basis sets.

http://dl.dropbox.com/u/808644/firefly_data.zip

Мay be this will be useful for you. I didn’t check this instruction, but it
seems similar to one I used.
http://ocikbws.uzh.ch/education/gamess/datfile.html#pltorb3d

P.S.
If you need i can make H20 files. I just send you that I already have - with
pentane

Denis

/////////////////////////////////////////////////////////////////////////////////////////////////
On Thu, May 13, 2010 at 10:21 PM, Geoffrey Hutchison <
geoff.hutchison@gmail.com> wrote:

  1. I don’t know if Avogadro could parse that data at all.

Avogadro does not yet parse GAMESS or MacMolPlt orbital data. If someone
would like to send me some example files, I can take a crack at it.

Best regards,
-Geoff

Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
avogadro-discuss List Signup and Options

7

So, this is the conclusion, with Avogadro I can see the structure
(coordinates) from firefly, but no molecular orbitals yet?

Thank you very much people, really thanks

2010/5/13 Denis Lyubimov lyubimov.denis@gmail.com

Hello.

Sorry I messed up. Firefly outputs in MacMolPlot files only coordinates, so
there is no need to play with it, and even more it outputs in PUNCH not,
*.gamout file

Here you can get zip file with two input,gamout and PUNCH files for
semi-empirical PM3 and ab initio 6-31G basis sets.

http://dl.dropbox.com/u/808644/firefly_data.zip

Мay be this will be useful for you. I didn’t check this instruction, but it
seems similar to one I used.
http://ocikbws.uzh.ch/education/gamess/datfile.html#pltorb3d

P.S.
If you need i can make H20 files. I just send you that I already have -
with pentane

Denis

/////////////////////////////////////////////////////////////////////////////////////////////////

On Thu, May 13, 2010 at 10:21 PM, Geoffrey Hutchison <
geoff.hutchison@gmail.com> wrote:

  1. I don’t know if Avogadro could parse that data at all.

Avogadro does not yet parse GAMESS or MacMolPlt orbital data. If someone
would like to send me some example files, I can take a crack at it.

Best regards,
-Geoff

Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
avogadro-discuss List Signup and Options

Avogadro-Discuss mailing list
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