On Sun, Nov 9, 2014 at 1:26 AM, Bajarang Kumbhar <kumbharbajarang.gmail.com>
wrote:
> Hi Dear AMBER USERS
> I have perform the Implicit simulation of protein and
> drug molecule, Further i would like to calculate the binding energy using
> MMPBSA and GB method but the most of tutorial show the explicit simulation
> data for MMPBSA/GB calculation.
> like this
>
> $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop -y
> *.mdcrd.
>
> my question is that, it is possible to perform the PB and GB calculation
> without the solvated.prmtop file.
>
Yes. The solvated prmtop is only used to strip solvent and ions from the
trajectory file. If you do not provide a solvated topology file, MMPBSA.py
will assume that you do not need to strip solvent and ions and will simply
run the calculation directly (but then, of course, the input trajectory
needs to be compatible with the complex topology file).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Nov 09 2014 - 06:30:02 PST
