AMBER Archive (2004)

Subject: Re: AMBER: Cannot read in sander

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

On Wed, May 26, 2004, 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 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.



================================================================== David A. Case | e-mail: 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 | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to