Yes, prmtop defines a bond to that proton.
What could be the reason that just that one proton doesn`t have
constrain on it?
Kind regards,
Antonija
Citiram Brian Radak <radak004.umn.edu>:
> 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
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
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--
Antonija Tomić
LKBK
Institut Ruđer Bošković
10 000 Zagreb
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Received on Wed Dec 19 2012 - 06:00:07 PST
