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
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Received on Sun Apr 24 2011 - 07:30:03 PDT
