Hello Jason and Bill:
thanks a lot for kind and helpful advices.
I visualized the complex.top + MMPBSA_complex.mdcrd.0 output file
from MMPBSA results, it seems that my crystal water was included in the
calculation. you can find a screenshot here;
http://dl.dropbox.com/u/56271062/mmpbsa.jpeg
The top T3P model messed up with problem in above figure....
However, my system was built with following configurations for tleap:
source leaprc.ff12SB
loadAmberParams frcmod.ionsjc_tip3p
loadamberparams ligand.frcmod
loadoff ligand.lib
ligand= loadpdb lig.pdb
receptor= loadpdb rec.pdb
complex = combine {receptor ligand}
set default PBRadii mbondi2
saveamberparm ligand lig.top lig.crd
saveamberparm receptor rec.top rec.crd
saveamberparm complex com.top com.crd
solvatebox complex TIP3PBOX 10.6
charge complex
addions complex Na+ 11
charge complex
saveamberparm complex com_sol.prmtop com_sol.inpcrd
quit
After the simulation, I run MMPBSA with following command:
MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
../com_sol.prmtop -cp ../com.top -rp ../rec.top -lp ../lig.top -y
../npt4.trj > log &
According to the Amber manual and your comments, the crystal waters
should NOT in the calculation, but I don't know why there were present
when I visualize the MMPBSA output in VMD....
thank you very much
best
Albert
On 04/03/2013 04:30 PM, Jason Swails wrote:
> Don't forget to modify "strip_mask" if you want to keep some water
> molecules. By default all waters (and ions) are stripped from the solvated
> trajectory.
>
> HTH,
> Jason
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Received on Wed Apr 03 2013 - 08:00:03 PDT
