AMBER Archive (2009)

Subject: [AMBER] mdfil: Error unknown flag during sander minimization

From: Workalemhu Berhanu (
Date: Tue May 26 2009 - 08:57:29 CDT

Dear all
I was trying to run sander minimization on my decapeptide whose structure I got form pdb. The creation of the topology file and the Cartesian coordinate using xleap went well but when I try to run sander minimization using the commands as in the tutorial (tutorial B1I) got the error message shown below.
$AMBERHOME/exe/sander -O -i -o G Decggvvia_gb_init_min.out GDecggvvia_vac.inpcrd GDecggvvia_vac.prmtop -r GDecggvvia_gb_init_min.rst

     mdfil: Error unknown flag: GDecggvvia_vac.inpcrd

     usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
                   [-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo -radii radii]
Consult the manual for additional options.
Thank you

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