AMBER Archive (2009)

Subject: Re: [AMBER] sander not working

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Jan 16 2009 - 08:58:50 CST

On Fri, Jan 16, 2009, archana sonawani wrote:

> I am preparing co-ordinate and topology files using xleap in
> amber10 and then run minimization using following command
>
> $AMBERHOME/exe/sander -O -i min1.in -o min1.out -c crd.md.23
>
> 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.

There is way too little information here for anyone to help. But since
you have similar sets of files, some of which work and some which don't,
you can probably track down the problem yourself. Slowly change the
inputs from what works towards what doesn't, and see if you can localize
the problem, e.g. the smallest change that breaks things.

...good luck...dac

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