[AMBER] QM/MM issue with boron containing compound (AMBER16)

From: Bodee Nutho <b.nutho.gmail.com>
Date: Thu, 10 May 2018 22:04:32 +0700

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
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