On Mon, 2014-04-07 at 17:05 +0530, Arunima Shilpi wrote:
> 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"
This was merely demonstrating that MMPBSA.py accepts wildcards on the
command-line. The command you should use depends on which files you
want to use for your analysis. In this case, since 1err_prod.mdcrd is
the only file whose name ends with ".mdcrd", the two options
-y *.mdcrd
-y 1err_prod.mdcrd
are completely equivalent. If there were two files 1err_prod.mdcrd and
1err_prod2.mdcrd, then the first command would select both and the
second would select only the first one.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Apr 07 2014 - 05:30:02 PDT
