AMBER Archive (2004)

Subject: Re: AMBER: error in antechamber

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Apr 07 2004 - 08:30:55 CDT

Hi Anshul,

I had the same problem. I have tried to modify Mopac 7 to antechamber in
order to get a result. The problem lies in the mopac.sh file as you might
have realized. Before that, I suggest you to test antechamber. And also
look at the following post, which helped me to run the test for
antechamber.

http://amber.ch.ic.ac.uk/archive/200401/0155.html

Here, it is describing you what to do in order to modify antechamber to
use mopac 7. (I am assuming the same thing is true for the other versions
of mopac)

The only problem is that when I run the test for antechamber, I ended up
with a lot of failures, and I posted a message to here AMBER list to know
whether that is normal or not.

In any case, the answer to your question lies in the 'mopac.sh' file,
which is a script telling antechamber what to do with Mopac. I wish that
this file was modified by the programmers who wrote antechamber, or gave
some descriptions on how to modify it.

Good luck... 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
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  - University of Rochester      -                              -
  - Hutchison Hall, Office B10   - 60 Crittenden Blvd. Apt. 232 -
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  ---------------------------------------------------------------

On Wed, 7 Apr 2004 anshul_at_imtech.res.in wrote:

> hi everyone,
> i am trying to generate parameters for a molecule using antechamber. for
> this i am using MOPAC5.010. when i run antechamber i get am error which is
> as follows
>
>
>
>
> antechamber -i atrazine.pdb -fi pdb -o atra.prep -fo prepi -c bcc
> Running: /usr/people/bvs/amber7/exe/mopac.sh ANTECHAMBER_MUL.MOP
> ANTECHAMBER_MUL.OUT /usr/people/bvs/amber7/exe/mopac.sh[11]:
> /usr/people/bvs/mopac5010mn/:  cannot execute
> Cannot open ANTECHAMBER_MUL.OUT , exit
>
>
> cna nyone help me with this. any suggestion is greatly appreciated.
> with regards,
> anshul
>
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