Hi everyone,
I'm trying to perform QM/MM MD on a boron-containing compound.
I did perform an equilibration of the complex for 1-ns using classical MD
simulation. Everything seems to be fine with this classical MD.
After that, I switched from running classical MD to QM/MM MD using PM6
Hamiltonian. I have found the problem with the reading of boron atom in
which boron atom turned to be an unknown element.
How should I solve this problem?
*My input file is like this:*
==========================================
QMMM simulation
&cntrl
imin=0,
ntx=5,
irest=1,
nstlim=200000,
dt=0.001,
ntf=2,
ntc=2,
temp0=300.0,
ntpr=200,
ntwx=200,
ntwr=200,
ioutfm=1,
iwrap=1,
cut=8.0,
ntb=2,
ntp=1,
ntt=1
pres0=1.0,
tautp=3.0,
ig=-1,
ifqnt=1,
/
&qmmm
qmmask='.2411-2480',
qmcharge=2,
qm_theory='PM6',
qmshake=1,
qm_ewald=0, qm_pme=0,
/
==========================================
*Error on CPU using sander is like this:*
==========================================
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 2411 C -4.4935 -2.8302 5.0316
QMMM: 2 2412 O -3.9974 -2.6315 3.6927
*QMMM: 3 2413 ^.^. -4.5185 -1.4741 2.8766*
QMMM: 4 2414 C -4.0804 -1.4976 1.2806
QMMM: 5 2415 N -2.6246 -1.2517 1.0995
QMMM: 6 2416 C -2.0848 -0.0660 0.7917
QMMM: 7 2417 C -0.5823 0.2605 1.2061
QMMM: 8 2418 N 0.3109 0.6983 0.1875
QMMM: 9 2419 C 0.5833 -0.1113 -0.7879
QMMM: 10 2420 O 0.7251 -1.2955 -0.4686
QMMM: 11 2421 C 0.8056 0.3465 -2.1101
QMMM: 12 2422 C 1.3613 -0.6292 -2.9928
QMMM: 13 2423 H 1.6053 -1.6014 -2.5906
QMMM: 14 2424 C 1.6019 -0.2230 -4.3365
QMMM: 15 2425 H 2.0376 -0.8853 -5.0699
QMMM: 16 2426 C 1.3101 1.0672 -4.7858
QMMM: 17 2427 H 1.4674 1.3287 -5.8218
QMMM: 18 2428 C 0.8913 2.0699 -3.9098
QMMM: 19 2429 H 0.6668 3.0736 -4.2395
QMMM: 20 2430 C 0.7361 1.7129 -2.5299
QMMM: 21 2431 H 0.3911 2.4409 -1.8106
QMMM: 22 2432 H 0.4110 1.6934 0.0463
QMMM: 23 2433 H -0.2345 -0.6510 1.6922
QMMM: 24 2434 C -0.5876 1.5090 2.2209
QMMM: 25 2435 H -1.3426 1.2900 2.9759
QMMM: 26 2436 H -0.9124 2.3662 1.6312
QMMM: 27 2437 C 0.6308 1.8633 2.9753
QMMM: 28 2438 C 0.6113 3.0441 3.6616
==========================================
------------------------------------------------------------
--------------------
3.1 QM CALCULATION INFO
------------------------------------------------------------
--------------------
QMMM: Atom number: 3 has atomic number -1.
QMMM: There are no PM6 parameters for this element. Sorry.
SANDER BOMB in subroutine qm2_load_params_and_allocate
UNSUPPORTED ELEMENT
QM PM6 NOT AVAILABLE FOR THIS ATOM
------------------------------------------------------------
--------------------
Thank you in advance
--
Bodee Nutho
Program in Biotechnology
17th floor, MHMK Building
Chulalongkorn University
Bangkok, THAILAND 10330
Tel: +66 (0)83 547 3066
Email: b.nutho.gmail.com
* <swaratchada.gmail.com>*
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Received on Thu May 10 2018 - 08:30:02 PDT
