AMBER Archive (2003)

Subject: Re: Antechamber

From: David A. Case (case_at_scripps.edu)
Date: Thu Jul 03 2003 - 12:36:47 CDT

On Thu, Jul 03, 2003, Shweta Sikri wrote:

> Thanks for response, I have already changed my mopac.sh file. I deleted '<'
> and '>' from the file which were around $1. Actually the problem is that
> when I use the command antechamber -i input -fi mol2 -o output -fo mol2 -c
> bcc, then it should generate a 'output' file of mol2 format which it never
> generates. It just generates ANTECHAMBER_MUL.MOP and ANTECHAMBER_MUL.OUT
> files. That's why I want to know the proper linking of mopac7 with Amber7.

We need more information to help:

1. Does your system pass the test suite? If so, the connection to mopac
is OK; if not, report what output you get (say for the "tp" test); in
particular, what is in the "mopac.out" file? This will help isolate the
problem.

2. What is in your ANTECHAMBER_MUL.OUT file? That should give you clues
about the problem, if it is indeed related to mopac. Can you do what mopac.sh
is doing by hand (on the command line)? What are the results? Are you sure
your version of mopac7 is running OK, outside of antechamber?

3. Use the "-s 2" option to antechamber to get more information on what it is
doing.

I have never had any luck with mopac7 myself, since many "modern" fortran
compilers don't like this code. Maybe someone else on the list will have some
suggestions.

..hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
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