Dear Sir
In the tutorial of amber for entropy calculation for estrogen-ligand the
following commands are given
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
1err.solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
ligand.prmtop -y *.mdcrd > progress.log
While in mpirun for the the following command is given
mpirun -np 3 MMPBSA.py.MPI -O -i mmpbsa_nm.in -o
FINAL_RESULTS_MMPBSA.dat -sp 1err.solvated.prmtop -cp complex.prmtop \
-rp receptor.prmtop -lp ligand.prmtop -y 1err_prod.mdcrd
> progress.log
Here you can see the difference in the command fro "-y *.mdcrd" it has
changed to "1err_prod.mdcrd"
Here I have query as to which command to be used over here.
I request you to kindly guide me with the command to be used for
entropy calculation
Regards
Arunima
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Received on Mon Apr 07 2014 - 05:00:02 PDT
