Dear all
Hello
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 GDecggvvia_gb_init_min.in -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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Received on Wed May 27 2009 - 01:09:46 PDT
