AMBER Archive (2009)

Subject: Re: [AMBER] sander not working

From: Carlos Simmerling (
Date: Fri Jan 16 2009 - 09:01:34 CST

you don't have a prmtop file specified here, but that's probably not
why you don't get any output.
if you run the job in the background (put $ at the end), then do
"top", does it show sander running?

sometimes it is easiest to put your sander command in a script and run
that, rather than typing it in each time. then you can diff the script
that works and the one that doesn't and see the differences.

On Fri, Jan 16, 2009 at 12:52 AM, archana sonawani
<> wrote:
> Hi,
> I am preparing co-ordinate and topology files using xleap in
> amber10 and then run minimization using following command
> $AMBERHOME/exe/sander -O -i -o min1.out -c
> The cursor just blinks and the min1.out is blank.
> when i use the co-ordinate and topology files for any example, the sander
> jobs run but when I make the files using xleap (focefield 99SB) which is
> similar to the co-ordinate and topology files from example, still sander
> dont run. I am puzzled why this happens?????????
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