Re: OpenBabel-discuss Digest, Vol 119, Issue 5

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Re: OpenBabel-discuss Digest, Vol 119, Issue 5

Torsten Sachse
Hi Vaibhav,

> What I meant is that it showed "bash: babel: command not found"
> But when I installed not as root then its working.

so it seems as if the directory, wo which babel and obabel are
installed, is not in your PATH environment variable (which contains all
the directories that are being searched whenever you execute a command
in bash, for example). So just add the directory to the PATH variable
and the directory that contains the openbabel libraries to the
LD_LIBRARY_PATH variable.

> Can you please suggest me on the following also?
> I want to get the last optimized geom from GAMESS output, but when I use
> the following command
> babel -igamin xyz.out -ogamin xyz-1.inp

I would suggest using -igamout when converting GAMESS output.

> I get the first geometry not the last optimized one.
> babel -H doesn't say anything on that.

If you already know that, say, the last geometry is number 22, then you
can run "babel -igamin xyz.out -ogamin xyz-1.inp -f 22 -l 22". At least
that's what openbabel suggested when I tried to convert an
xyz-trajectory to the gamin format. I don't know whether there is a way
to get the last geometry without knowing its index.

Best,
Torsten

On Mon, 25 Apr 2016, [hidden email] wrote:

> Hi Pascal and all,
> I have given the following response to suggestions by Fredrik and others.
> I think there is a delay in my responses getting accepted and viewed by
> members of the group.
> Not sure why, this should happen?
> thanks for your suggestions.
> Vaibhav??
>
> Hi Fredrik and all,
> What I meant is that it showed "bash: babel: command not found"
> But when I installed not as root then its working.
> Can you please suggest me on the following also?
> I want to get the last optimized geom from GAMESS output, but when I use
> the following command
> babel -igamin xyz.out -ogamin xyz-1.inp
>
> I get the first geometry not the last optimized one.
> babel -H doesn't say anything on that.
> Any suggestion is highly appreciated.
> thank you

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Re: OpenBabel-discuss Digest, Vol 119, Issue 5

Vaibhav Dixit

Hi

​All,

I tried the following
​​
babel -igamin xyz.out -igamin xyz.
​i
​np -f 22​

babel -igamin xyz.out -igamin xyz.​i​np -f 22​
​ -I 22

but got the same message in the use of both commands

0 molecules converted

2 audit log messages

Where I can find these message?​

​I thought that this utility is available for GAUSSIAN output only, is it?

If this does work I will write a short script to find how many "FINAL" are there in the output ​and use that number to get the geometry.

Else it will be slightly complicated.

thanks

vaiibhav

On Apr 25, 2016 17:48, "Torsten Sachse" <[hidden email]> wrote:
Hi Vaibhav,


What I meant is that it showed "bash: babel: command not found"
But when I installed not as root then its working.

so it seems as if the directory, wo which babel and obabel are
installed, is not in your PATH environment variable (which contains all
the directories that are being searched whenever you execute a command
in bash, for example). So just add the directory to the PATH variable
and the directory that contains the openbabel libraries to the
LD_LIBRARY_PATH variable.


Can you please suggest me on the following also?
I want to get the last optimized geom from GAMESS output, but when I use
the following command
babel -igamin xyz.out -ogamin xyz-1.inp

I would suggest using -igamout when converting GAMESS output.


I get the first geometry not the last optimized one.
babel -H doesn't say anything on that.

If you already know that, say, the last geometry is number 22, then you
can run "babel -igamin xyz.out -ogamin xyz-1.inp -f 22 -l 22". At least
that's what openbabel suggested when I tried to convert an
xyz-trajectory to the gamin format. I don't know whether there is a way
to get the last geometry without knowing its index.

Best,
Torsten


On Mon, 25 Apr 2016, [hidden email] wrote:

Hi Pascal and all,
I have given the following response to suggestions by Fredrik and others.
I think there is a delay in my responses getting accepted and viewed by
members of the group.
Not sure why, this should happen?
thanks for your suggestions.
Vaibhav??

Hi Fredrik and all,
What I meant is that it showed "bash: babel: command not found"
But when I installed not as root then its working.
Can you please suggest me on the following also?
I want to get the last optimized geom from GAMESS output, but when I use
the following command
babel -igamin xyz.out -ogamin xyz-1.inp

I get the first geometry not the last optimized one.
babel -H doesn't say anything on that.
Any suggestion is highly appreciated.
thank you

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Re: OpenBabel-discuss Digest, Vol 119, Issue 5

Geoff Hutchison
​​
babel -igamin xyz.out -igamin xyz.
​i
​np -f 22​

I don't know what kind of file xyz.out is, but I doubt that it's a GAMESS input.

Try:

obabel xyz.out -O xyz.inp -f 22 -ogamin

Usually the ".out" format code is smart enough to figure out the kind of file you hand it.

Best regards,
-Geoff

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Re: OpenBabel-discuss Digest, Vol 119, Issue 5

Vaibhav Dixit
Hi,
It turned out simpler than expected.

babel xyz.out -O xyz.inp

is giving me the desired last geometry in GAMESS input format.
I have manually gone to the last geom using wxMacMolPlt, saved is as test.inp and compared it with that generated by babel.
they have identical coordinates. Rather babel gives values with 10 decimals while wxMacMolPlt gives only 3, it may or may not be important based on what we do with these coordinates.

thanks all for inputs.
vaibhav


On Tue, Apr 26, 2016 at 8:45 AM, Geoffrey Hutchison <[hidden email]> wrote:
​​
babel -igamin xyz.out -igamin xyz.
​i
​np -f 22​

I don't know what kind of file xyz.out is, but I doubt that it's a GAMESS input.

Try:

obabel xyz.out -O xyz.inp -f 22 -ogamin

Usually the ".out" format code is smart enough to figure out the kind of file you hand it.

Best regards,
-Geoff



--
With Regards.

Dr. Vaibhav A. Dixit, (M.S. and Ph.D.: NIPER, Postdoc: AstraZeneca, UK and IISc, Bangalore)
Associate Professor,
Department of Pharmaceutical Chemistry,
School of Pharmacy & Technology Management,
SVKM's NMIMS, 
Mukesh Patel Technology Park
Babulde, Bank of Tapi River,
Mumbai-Agra Road,
Shirpur, Dist. Dhule -425405
India.
Email: [hidden email]
www.nmims.edu
+91-7709129400.
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra

Please consider the environment before printing this e-mail

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