You have not given -c & -p before coordinate and topology input files.
On Tue, May 26, 2009 at 6:57 PM, Workalemhu Berhanu
<wberhanu.mail.ucf.edu>wrote:
> 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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--
Shubhra Gupta
Information Officer,
Department of Bioinformatics & Structural Biology
Indian Institute of Advanced Research
Koba Village
Gandhinagar 382007 Gujarat
Phone: 91-79-30514154
Email: shubhg.iiar.res.in
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Received on Wed May 27 2009 - 01:15:47 PDT
