You need to place a '-' in front of O to designate the overwrite command.
Thus, your command for running sander should look like this,
$ sander -O -i polyAT_vac_init_min.in -o polyAT_vac_init_min.out -p
polyAT_vac.prmtop -c polyAT_vac.inpcrd -r polyAT_vac_init_min.rst
Good luck!
-Bill Miller
On Thu, Feb 18, 2010 at 8:54 AM, vaibhav jain <xtreme.vaibhav.gmail.com>wrote:
> hi ,
> After giving this command for running sander, following error is coming.
>
> $ sander O -i polyAT_vac_init_min.in -o polyAT_vac_init_min.out -p
> polyAT_vac.prmtop -c polyAT_vac.inpcrd -r polyAT_vac_init_min.rst
>
> mdfil: Error unknown flag: O
>
> 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 -y inptraj]
> Consult the manual for additional options.
>
>
> So how to resolve this problem.
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Received on Thu Feb 18 2010 - 06:00:05 PST
