Hi Antonija,
Does the prmtop define a bond to that proton? My understanding is that
SHAKE takes its constraint values from the underlying force field (which is
otherwise ignored). The only explanation I can think of off hand is that
the proton being transferred doesn't actually have a constraint on it.
Regards,
Brian
On Wed, Dec 19, 2012 at 8:32 AM, Antonija Tomić <Antonija.Tomic.irb.hr>wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
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Received on Wed Dec 19 2012 - 06:00:06 PST
