Dear Amber Users,
I am using SHAKE algorithm for QM hydrogen atoms during QM/MM MD
simulation in Amber 12 (qmshake = 1, using SCC-DFTB method). Input
file is given at the end. Prior to this, classical minimization,
equilibration and MD simulations were performed.
The question is why my substrate molecules gets deprotonated by one of
glutamate residues, both described quantum mechanically? Substrate
molecule is dipeptide, and its N-terminus (NH3+ group) gets
deprotonated. I know that this is chemically possible, but shouldn't
SHAKE prevent this?
Kind regards,
Antonija
INPUT:
QM/MM molecular dynamics run
&cntrl
imin=0, irest=0, ntx=1, ig=-1,
ntb=2, ntp=1, cut=11.0, ntc=2, ntf=2,
tempi=280.0, temp0=280.0, ntt=3, gamma_ln=1.0,
nstlim=10000, dt=0.001, ntpr=100, ntwx=100, ntwr=100, ntwe=100,
ifqnt=1,
/
&qmmm
iqmatoms=11365,
7904,7905,7906,7907,7908,7909,
7035,7036,7037,7038,7039,7040,
7092,7093,7094,7095,7096,7097,7098,7099,7100,7101,7102,
7015,7016,7017,7018,7019,7020,7021,7022,7023,7024,7025,
11366,11367,11368,11369,11370,11371,11372,11373,11374,11375,11376,11377,11378,11379,11380,11381,11382,11383,11384,11385,11386,11387,11388,11389,11390,11391,11392,11393,11394,11395,11396,11397,11398,11399,11400,11401,11402,11403,11404,11405,11406,11407,11408,11409,11410,11411,11412,11413,11414,11415,11416,11417,11418,11419,11420,11421,11422,11423,11424,11425,11426,11427,11428,11429,11430,11431,11432,11433,11434,
43262,43263,43264,
58010,58011,58012,
56633,56634,56635,
39071,39072,39073,
78218,78219,78220,
44666,44667,44668
qm_theory='SCC-DFTB',
dftb_3rd_order='PA',
qmcharge=3,
verbosity=0,
qmshake=1,
qmcut=11.0, qm_ewald=1,qm_pme=1,
scfconv=1.0D-8, tight_p_conv=0,
verbosity=0,writepdb=1,adjust_q=2,dftb_telec=0.0
/
--
Antonija Tomić
LKBK
Institut Ruđer Bošković
10 000 Zagreb
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Received on Wed Dec 19 2012 - 06:00:04 PST
