Hello! I try to use QMMM MD method realized in Amber10, and i've got a
problem.
QMMM minimization and simulation of my ligand in water box (ligand is QM
part) run very well, but in minimization of ligand bound with protein (QM
part is ligand or "ligand+key amino acid residue"), ligand exploded with
warnings in output:
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 = -0.8502E+06 DeltaE = 0.1024E-07 DeltaP = 0.2569E-08
QMMM: Smallest DeltaE = 0.1013E-07 DeltaP = 0.2645E-08 Step = 997
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -2.4989E+05 1.3498E+01 1.8696E+02 CD2 12005
BOND = 287.5026 ANGLE = 1680.2157 DIHED =
7289.6363
VDWAALS = 9711.0237 EEL = -305100.5093 HBOND =
0.0000
1-4 VDW = 3111.1525 1-4 EEL = 32480.0419 RESTRAINT =
142.9937
PM3ESCF = 511.4157
EAMBER = -250029.5209
Protein-ligand complex is based on crystallographic structure, thus, i
believe that starting conformation is good.
I've tried cut off 8, 9, 10; AM1 and PM3; SHAKE and NOSHAKE minimization.
Example of input file is attached.
Thanks a lot!
--
Dmitry Nilov,
Lomonosov Moscow State University
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Received on Tue Mar 30 2010 - 08:00:03 PDT
