I use Amber QM/MM to simulate the enzyme catalysis, the catalytic process
involves the bond broken and formation, so for the QM part, I did not use qmshake.
First,
I simulate the enzyme-ligand system using the traditional MM method, then
taking the complex structure from the MM simulation as the initial structure,
QM/MM was run. I first run the MM energy minimization, then carried out the
heating progress,
heating
&cntrl
imin=0,irest=0,ntx=1,
nstlim=25000,dt=0.002,
ntc=2,ntf=2,pencut=-0.001,
cut=10.0, ntb=1,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=2.0,
tempi=0.0, temp0=300.0,
nmropt=1,
ifqnt=1
/
&qmmm
iqmatoms=2058,2059,2060,2061,2062,2471,2472,2473,2474,2475,2476,2477,2468,2469,2470,2907,2908,2909,2910,2911,2912,
3317,3318,3319,3320,3321,3322,2432,2433,2434,2435,2436,2437,2438,2439,2440,2441,4790,4791,4792,4793,
4794,4795,4796,5475,5476,5477,3730,3731,3732,3733,3734,3735,4474,4475,4476,4477,4478,4479,4480,4481,4482,
5452,5453,5454,5455,5456,5457,5458,5459,5460,5461,5462,5463,5464,5465,5466,5467,5468,5469,
qmcharge=0,
qmshake=0,
qm_ewald=1, qm_pme=1
/
&wt TYPE='TEMP0', istep1=0, istep2=25000,
value1=0.1, value2=300.0, /
&wt type='REST',
istep1=0,istep2=5000,value1=0.1,
value2=1.0,
/
&wt type='REST',
istep1=5001,istep2=25000,value1=1.0,
value2=1.0,
/
&wt TYPE='END' /
LISTOUT=POUT
DISANG=RST.wc
After 2500 steps, the following error occurred:
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 =
-0.2065E+07 DeltaE =
0.2495E+02 DeltaP =
0.8346E-01
QMMM: Smallest
DeltaE =
0.8698E+00 DeltaP =
0.1194E-01 Step =
96
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 =
-0.2066E+07 DeltaE =
0.4190E+01 DeltaP =
0.6703E-01
QMMM: Smallest
DeltaE =
0.5521E+00 DeltaP =
0.5861E-01 Step =
56
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 =
-0.2067E+07 DeltaE =
0.1638E+02 DeltaP =
0.3070E-01
QMMM: Smallest
DeltaE =
-0.1253E-04 DeltaP =
0.5759E-07 Step =
77
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 =
-0.2067E+07 DeltaE =
-0.5213E+02 DeltaP =
0.9210E-01
QMMM: Smallest
DeltaE =
0.1905E-02 DeltaP =
0.2358E-01 Step =
457
vlimit exceeded for step
2509; vmax =
21.0047
vlimit exceeded for step
2510; vmax =
49.6459
vlimit exceeded for step
2511; vmax =
45.8189
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are :
0
3
2245
4494
4497
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
Therefore, how can I solve the problem?
How should I do to relax the QM part of the
system?
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Received on Sun Feb 12 2012 - 21:30:03 PST
