When you used the command line:
sander -O -i sander_com.in -o sander_com.1.out -c ./snapshot_com.crd.1 -p
./37578.prmtop not successful
you left the "not successful" at the end. Sander thought that "not" was a
flag you were trying to use, but obviously this isn't a proper flag. Drop
the "not successful" from the end of the command line argument and try
again.
-Bill
On Sun, Apr 24, 2011 at 10:07 AM, Andrew Voronkov <drugdesign.yandex.ru>wrote:
> Dear Amber users, I have tried to use mmpbsa.pl and I have got the next
> errors:
>
> " $AMBERHOME/exe/mm_pbsa.pl 37578_energy.mmpbsa > 37578_energy.log
> /home/amber10/exe/sander -O -i sander_com.in -o sander_com.1.out -c
> ./snapshot_com.crd.1 -p ./37578.prmtop not successful"
>
>
> Then I have tried to do it directly without mmpsa.pl script and got the
> error below which is not listed in Amber archive. What does it mean, flag
> "not"?
>
> [voronkov.t60-2 37578]$ sander -O -i sander_com.in -o sander_com.1.out -c
> ./snapshot_com.crd.1 -p ./37578.prmtop not successful
>
> mdfil: Error unknown flag: not
>
> 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.
>
> Sincerely yours,
> Andrey
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Apr 24 2011 - 08:00:04 PDT
