Hello Ambers,
I have been doing QMMM (using a development version of Amber10
sander furnished by Ross Walker). The basic design is steered
QMMM with the steered coordinate along a proposed scissile C-N
bond. I have been having a lot of trouble with this calculation
when I incorporate close waters into the QM region. These
problems seems to be of two kinds: (1) the QM water(s) diffuse
away from the enzyme active site, (2) the QM calculation (SCC-DFTB
w/o dispersion corrections) has great difficulty achieving SCF.
I can understand (I think) the reasons for both of these problems.
The diffusion problem is obvious, the SCF problem is probably
secondary to the diffusion, the waters are too far away from the
remainder of the QM region.
My question is whether anyone has suggestions to bypass these
issues? (I already know I can restrain the waters, but I have
some questions in my mind about the shape of the restraint. These
question involve the restraint distance and the "steepness" of the
parabolic restraint component. I don't want to bias the
calculation whose whole purpose is to reveal possible reaction
pathways.)
I would appreciate any comments people might have. I have
included the "in" file and the dist.RST file for my last run.
It bombed with:
****************************************************
ERROR: QM region + cutoff larger than box dimension:
QM-MM Cutoff = 9.0000
Coord Lower Upper Size Box(a,b,c)
X -27.285 46.641 73.926 73.802
Y 21.004 67.921 46.917 78.348
Z 9.986 54.744 44.758 70.532
****************************************************
SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f>
QM region + cutoff larger than box
cannot continue, need larger box.
I think this is related to the diffusion problem.
Bud Dodson
--
M. L. Dodson
Email: mldodson-at-houston-dot-rr-dot-com
Phone: eight_three_two-56_three-386_one
1vas, run steered QMMM, dropping snapshots along the way
&cntrl
ntx = 5, irest = 1, ntrx = 1, ntxo = 1,
ntpr = 100, ntwx = 400, ntwv = 400,
ntwe = 0,
ntf = 2, ntb = 1,
cut = 9.0, nsnb = 25,
nstlim = 100000,
t = 0.0, dt = 0.0005,
ntt = 1, tautp = 10.0,
temp0 = 300.0, tempi = 300.0,
ig = 71277,
tautp = 0.5,
vlimit = 20.0,
ntc = 2,
jar = 1,
ifqnt = 1,
nmropt = 1,
iwrap = 1,
/
&qmmm
iqmatoms = 1,2,3,4,5,6,7,8,9,10,11,12,13,14,356,357,358,359,360,361,
2465,2466,2467,2468,2469,2470,2471,2472,2473,
2474,2475,2476,2477,2478,2479,2480,2481,2482,2483,2484,2485,
2486,2487,2488,2489,2490,2491,2492,2493,
2501,2502,2503,2504,2505,2506,2507,2508,
2509,2510,2511,2512,2513,2514,2515,2516,2517,2518,2519,2520,
2521,2522,2523,2524,2525,
3382,3383,3384,
25783,25784,25785,
qmcut = 9.0,
qmtheory = 7,
dftb_doscc = 1,
dftb_disper = 0,
qmcharge = 0,
peptide_corr = 0,
qmshake = 0,
writepdb = 1,
adjust_q = 2,
/
&wt type='DUMPFREQ', istep1 = 500,
/
&wt type='END',
/
DISANG=dist.RST
DUMPAVE=dist_vs_t
LISTIN=POUT
LISTOUT=POUT
&rst iat=2472,2477, r2=1.50, rk2=5000., r2a=3.70,
/
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Received on Wed Aug 01 2007 - 06:07:26 PDT
