Hi all,
I tried to do QM/MM-GBSA calculation directly over the trajectory by setting
imin = 5, maxcyc=1. I tried to the way described in one of the previous
post
http://archive.ambermd.org/201012/0510.html
My first snapshot seems to run fine but after that I am getting convergence
problem for SCF calculation. My input file looks like -
--------------------------
MMGBSA.in--------------------------------------------------------------------------
QM/MM GBSA, Complex
&cntrl
irest=0,ntx=1,
imin=5,maxcyc=1,drms=0.0001,
ntpr=1,ntwx=0,ntwv=0,ntwe=1,
ntf = 1, ntb = 0,
igb = 5, dielc = 1.0,
cut = 1000.0, nsnb = 10,
intdiel= 1.0, extdiel=80.0,
rgbmax = 1000.0, gbsa = 0,
ifqnt=1
/
&qmmm
qmmask=":76,267-268" ! (QM region)
qmcharge=0, !(Charge on QM region)
qm_theory="PM3", !(Use the DFTB semi-empirical Hamiltonian)
qmcut=1000.0, !(Use1000 angstrom cut off for QM region)
printcharges=1, !print QM charges
dftb_telec=100.0 !temperature for fermi func.
/
------------------------------------------------------------------------------------------------------------------
ans the output file have warning and problems in calculation :
------------------------
xxxxx.out---------------------------------------------------------------------------
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.8615E+05 1.8659E+01 1.8766E+02 HD1 3730
BOND = 2838.0446 ANGLE = 1922.7114 DIHED =
2601.7086
VDWAALS = -607.0161 EEL = -33470.2770 EGB =
-172190.6556
1-4 VDW = 903.7275 1-4 EEL = 12068.1168 RESTRAINT =
0.0000
PM3ESCF = -218.7922
minimization completed, ENE= -.18615243E+06 RMS= 0.186588E+02
minimizing coord set # 2
QMMM: WARNING!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: Job will continue with unconverged SCF. Warning energies
QMMM: and forces for this step will not be accurate.
QMMM: E = -0.5100E+06 DeltaE = -0.6838E-01 DeltaP = 0.2281E-03
QMMM: Smallest DeltaE = -0.5410E-01 DeltaP = 0.2281E-03 Step = 810
Maximum number of minimization cycles reached.
QMMM: WARNING!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: Job will continue with unconverged SCF. Warning energies
QMMM: and forces for this step will not be accurate.
QMMM: E = -0.5100E+06 DeltaE = 0.9092E-01 DeltaP = 0.2581E-03
QMMM: Smallest DeltaE = -0.5645E-01 DeltaP = 0.2389E-03 Step = 21
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 5.7854E+17 2.6700E+17 6.0242E+19 O 16760
BOND = ************* ANGLE = 380659.4980 DIHED =
14424.2567
VDWAALS = ************* EEL = 163422.6168 EGB =
-2195805.9753
1-4 VDW = ************* 1-4 EEL = -5450.7695 RESTRAINT =
0.0000
PM3ESCF = 2227.5540
minimization completed, ENE= 0.57854326E+18 RMS= 0.267003E+18
minimizing coord set # 3
Could you please point me out if there is any mistake with the input
parameters, or its is because of poor starting geometry and I need to relax
the system in much better way. My QM region have one Trp from protein and
ligand is me-al-L-fucoside.
any suggestions ??
Sincerely
mish
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Received on Fri Jan 28 2011 - 04:00:02 PST
