AMBER Archive (2009)

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

From: David A. Case (
Date: Tue May 26 2009 - 09:05:37 CDT

On Tue, May 26, 2009, Workalemhu Berhanu wrote:

> $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]

As the usage statement indicates, all filenames are preceded by a flag. You
need a "-c" before "GDecggvvia_vac.inpcrd" and a "-p" before


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