Dear amber users,
I’m trying to run a QM/MM MD of a protein with its ligand and a Mg2+ ion in explicit solvent using the DFTB Hamiltonian. I’m getting the following error:
DFTB DISPERSION: Slater-Kirkwood dispersion switched on.
| Dispersion parameters read from file:
| /usr/local/amber/amber16/dat/slko/DISPERSION.INP_ONCHSP
Atom: N
h1 = 1.030 1.030 1.090 1.090
h2 = 3.800 3.800 3.800 3.800
Ni0 = 2.820
Atom: H
h1 = 0.386 0.386 0.000 0.000
h2 = 3.500 3.500 3.500 3.500
Ni0 = 0.800
Atom: C
h1 = 1.382 1.382 1.382 1.064
h2 = 3.800 3.800 3.800 3.800
Ni0 = 2.500
Atom: O
h1 = 0.560 0.560 0.000 0.000
h2 = 3.800 3.800 3.800 3.800
Ni0 = 3.150
Dispersion parameters for atom Mg not found.
SANDER BOMB in subroutine <qm2_dftb_dispersionread> qm2_dftb_dispersionread.f
Missing dispersion parameter.
Exiting.
But according to the amber16 manual, the dispersion correction is such that:
dftb_disper Flag turning on (1) or off (0) the use of a dispersion correction to the DFTB/SCC-DFTB energy. Requires qm_theory=DFTB. It is assumed that you have the file DISPERSION.INP_ONCHSP in your $AMBERHOME/dat/slko/ directory. This file must be downloaded from the website www.dftb.org, as described in the beginning of this chapter. Not available for the Zn atom. (Default = 0)
Although the DISPERSION.INP_ONCHSP file looks like:
O 0.560 0.560 0.000 0.000 3.8 3.8 3.8 3.8 3.15
N 1.03 1.03 1.090 1.090 3.8 3.8 3.8 3.8 2.82
C 1.382 1.382 1.382 1.064 3.8 3.8 3.8 3.8 2.5
H 0.386 0.386 0.000 0.000 3.5 3.5 3.5 3.5 0.8
P 1.6 1.6 1.6 1.6 4.7 4.7 4.7 4.7 4.5 !PO4
S 3.0 3.0 3.0 3.0 4.7 4.7 4.7 4.7 4.8 !S not SO2
So if I understand it correctly, dispersion corrections are available for C, N, O, H, P, S only.
So I was wondering if I’m missing something such that it is generating this error or if there is a way to generate such parameters for Mg ion that I could include in the dispersion file (as suggested in the following thread by Gustavo Seabra
http://archive.ambermd.org/200905/0194.html).
Here is my input file:
Constant Temp 300K MD
&cntrl
imin=0,
irest=1, ntx=5,
ntb=2, pres0=1.0, ntp=1, taup=1.0,
cut=12.0,
tempi=300.0, temp0=300.0,
ntt=3, gamma_ln=2.0, ig=-1,
nstlim=50000, dt=0.001,
ntpr=250, ntwx=200, ntwr=500, ioutfm=1,
ntc=2, ntf=2,
noshakemask = '.2828-2851,2941-2946,11908-11910,14608-14610',
ntr=1,
restraintmask = ':170,185,@CA,C,N',
restraint_wt=5.0,
ifqnt=1,
/
&qmmm
qmmask=':179,196-197,3185,4085',
qmcharge=-1,
qm_theory='DFTB',
dftb_disper=1, dftb_3rd_order='PR', dftb_telec=100,
qmshake=0,
qmcut=8.0,
/
Thank you in advance for any insight in this subject,
Sincerely,
Ruth
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Received on Thu Nov 10 2016 - 06:30:03 PST
