Hi,
I'm trying to determine the Energy of the complex only using mmpbsa. in
doing so i'm comparing 2 runs where:
#mmpbsa.in
nput file for running PB and GB
&general
verbose=1,
receptor_mask=':1-192',
ligand_mask=':193-384'
/
&gb
igb=5, saltcon=0.100
/
&pb
istrng=0.100,
radiopt=0
/
Looking at the Energies I get two very different results and was wondering
if they should be the same actually.
1) the ligand, receptor and complex are all included.
nohup mpirun -np 16 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o
FINAL_RESULTS_MMPBSA.dat -sp prmtop -cp com.prmtop -rp rec.prmtop -lp
lig.prmtop -y ../*.mdcrd > benchmarks.log &
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -2772.0879 64.4476 2.8822
EEL -26117.3304 242.6761 10.8528
EGB -7799.0717 244.1382 10.9182
ESURF 112.7079 6.8321 0.3055
G gas -28889.4183 199.5336 8.9234
G solv -7686.3638 248.8984 11.1311
TOTAL -36575.7821 76.8913 3.4387
2) only the complex is flagged
nohup mpirun -np 16 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o
FINAL_RESULTS_MMPBSA.dat -sp prmtop -cp com.prmtop -y ../*.mdcrd >
benchmarks.log &
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 1056.8691 25.5803 1.1440
ANGLE 3229.6268 43.1459 1.9295
DIHED 4289.7506 23.2319 1.0390
VDWAALS -2698.5830 66.0139 2.9522
EEL -26401.6751 173.8585 7.7752
1-4 VDW 1259.7356 14.1568 0.6331
1-4 EEL 21641.9617 42.1481 1.8849
EGB -7567.5331 162.8158 7.2813
ESURF 121.7999 7.5300 0.3368
G gas 2377.6856 172.8013 7.7279
G solv -7445.7332 164.8591 7.3727
TOTAL -5068.0476 73.0275 3.2659
any insight would be appreciated. thanks.
Dan
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 21 2016 - 13:00:03 PDT
