Well, it turns out my qmcharge parameter was wrong as it is not the total
charge of peptide, but the total charge of QM region! I changed it to one
and the error is gone now. Thanks.
Best,
Sam
On Mon, Apr 10, 2017 at 12:04 PM, Samaneh Ghassabi Kondalaji <
saghassabikondalaji.mix.wvu.edu> wrote:
> Dear Amber Users and Developers
> I am attempting to run a Steered MD simulation (SMD) (QM/MM at DFTB) in
> order to calculate the pKa value of a single amino acid residue in vacuum.
> It is worth mentioning that my unusual system is a triply-charged peptide
> with four Lysine residues carrying the charges that represents the solution
> phase charge states (LYS: -NH3+) even though my simulation is in vacuum. I
> am trying to monitor the CV value (http://ambermd.org/tutorials/
> advanced/tutorial10/) between the NZ atom on Lysine 12 and an Oxygen atom
> of a single tip3p water. In order to generate the system I solvated the
> peptide in a tip3p water box, using vmd determined the closest water
> molecule to one of the HZ atoms (-NH3+ Lysine 12), using cpptraj stripped
> all the water molecules except the target water and performed an energy
> minimization in vacuum. Using the fallowing parameters in the input file, I
> run a QM/MM equilibration in vacuum with QM mask on the target Lysine and
> the single water molecule:
>
> LYS12H2O: qmmm equilibration MD
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 0,
> cut = 20.0,
> tempi = 300.0,
> temp0 = 300.0,
> ntt = 3,
> gamma_ln = 1.0,
> ntf = 2, ntc = 2, tol = 0.00001,
> dt = 0.0005,
> ntpr = 100, ntwr=100, ntwx = 100,
> nstlim = 500000,
> ifqnt = 1,
> nmropt = 1,
> /
> &qmmm
> qmmask=':12, 23', !QM region mask LYS 12 and a SINGLE WATER, residue 23
> qmcharge=3, ! Total charge of the peptide
> qm_theory='DFTB',
> qmshake=0,
> tight_p_conv=0,
> scfconv = 0.100E-08,
> qmcut= 20.0,
> writepdb=1,
> /
> /
> &wt type='DUMPFREQ', istep1 = 5000,
> /
> &wt type='END',
> /
> DISANG=Dist_RST.dat
> DUMPAVE=Dist_vs_time
> LISTIN=POUT
> LISTOUT=POUT
>
> my Dist_RST.dat file contains:
> #
> # 12 LYS NZ 23 WAT O 2.5
> &rst
> iat= 139,270, r1= 2.4, r2= 2.5, r3= 2.5, r4= 2.6, rk2=1000.0,
> rk3=1000.0,
> /
> However, when I run the equilibration, I get this warning (output file is
> attached)
> QMMM SCC-DFTB: !!!! ============= WARNING ============= !!!!
> QMMM SCC-DFTB: Convergence could not be achieved in this step.
> QMMM SCC-DFTB: The calculation will continue, but energies and
> QMMM SCC-DFTB: forces for this step will not be accurate.
>
> I carefully tried changing the DFTB_TELEC value to 100, But I am still
> getting the same warning. I don't know at this point if the simulation
> parameters need to be changed or there is something wrong with my initial
> structure. Any suggestions would be greatly appreciated.
> Best Regards,
> Sam
>
>
>
> --
> *Samaneh ghassabi kondalaji*
> *PhD student in Chemistry*
> *555 CRL, Chemistry department*
> *West Virginia University *
> *Morgantown, USA*
>
> *E-mail: **saghassabikondalaji.mix.wvu.edu*
> <saghassabikondalaji.mix.wvu.edu>
>
>
--
*Samaneh ghassabi kondalaji*
*PhD student in Chemistry*
*555 CRL, Chemistry department*
*West Virginia University *
*Morgantown, USA*
*E-mail: **saghassabikondalaji.mix.wvu.edu*
<saghassabikondalaji.mix.wvu.edu>
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Received on Mon Apr 10 2017 - 10:00:02 PDT
