AMBER Archive (2004)

Subject: Re: AMBER: Cannot read in sander

From: David A. Case (case_at_scripps.edu)
Date: Thu May 27 2004 - 10:11:03 CDT

On Wed, May 26, 2004, bybaker_at_itsa.ucsf.edu wrote:
>
> Thank you for the suggestions. I guess that the problem was related to
> the quota limitation of my account. I had my account size increased, and
> the sander went through. But I got another problem, no result from the
> test run. I don?t know what happened. The ?model1-1.inpcrd? and
> ?model1-1.prmtop? contain the data, and my min.in is ?Minimization Test
> run1^M &cntrl^M imin=1, maxcyc=200^M ntpr=5^M &end?. The amber said
> ?Could not find cntrl namelist?, I don?t know what this mean.
>
>
> Here is the input file:
>
> Minimization Test run1^M &cntrl^M imin=1, maxcyc=200^M ntpr=5^M &end
> Could not find cntrl namelist

Looks like your line endings are messed up. It could be that you created
the input file on a PC and ran the job on Unix? Or vice versa? As you can
see from the above, your entire input file is on one line, and is treated
as a "title". The things that are separated by "^M" above should be on
separate lines.

...dac 

-- 

==================================================================
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:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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