AMBER Archive (2004)

Subject: RE: AMBER: Problem with sander - Error on Open

From: Thomas E. Cheatham, III (
Date: Thu Jul 08 2004 - 21:18:10 CDT

> cat <<eof >mdin
> mimimize
> &cntrl
> imin=1, maxcyc=100, rbornstat=1,
> cut=999.0, igb=5, saltcon=0.2,
> ntpr=1, ntx=1, ntb=0, dt=0.001, gbsa=1,
> nstlim = 1000, irest=0,
> &end
> eof
> sander -O -i mdin \
> -o sample.out -c sample.crd -p

(1) make sure your default shell did not change.
    [you have a sh or csh script above. You can cat /etc/passwd | grep mike
    assuming mike is your username. The last entry should be the shell
    you are running... If it is not /bin/sh, csh, or tcsh, you can start
    a csh shell by typing csh]

(2) type "which sander" to make sure that sander is in your path

(3) make sure that the "mdin" file was actually created. In general if
you use a script and there are problems, try doing each step by hand to
make sure all is well. If this is in a script, make sure


is the top line or whatever the path is to the appropriate shell you want
to apply.

This is likely a UNIX problem and not a sander problem.

Good luck.

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