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>
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Received on Mon Apr 10 2017 - 09:30:03 PDT
