Dear Amber community,
I have a system of 67 Decanoate molecules (with the corresponding 67 Na+) in water solution. I would like to do QM/MM to a couple of frames in a limited region of the system and by using PM6 there seems to be no problem. I would like to use another Hamiltonian for comparison purposes, and the DFTB3 seemed to be a good choice. Since the system have organic molecules and sodium ions, I download the package 3ob-3-1.tar.xz<
https://dftb.org/fileadmin/DFTB/public/slako/3ob/3ob-3-1.tar.xz> from
https://dftb.org/parameters/download/3ob/3ob-3-1-cc, decompress it and put it in the same directory with the rest of the simulation files. After running it, I get the following message:
Parameter files:
TYP (AT) TYP (AT) SK integral FILE
| 1 1 (Na) 1 (Na) /appl/soft/chem/amber/20-gcc/dat/slko/3ob-3-1/Na-Na.skf
| 2 1 (Na) 2 (C ) /appl/soft/chem/amber/20-gcc/dat/slko/3ob-3-1/Na-C.skf
| 3 1 (Na) 3 (O ) /appl/soft/chem/amber/20-gcc/dat/slko/3ob-3-1/Na-O.skf
| 4 1 (Na) 4 (H ) /appl/soft/chem/amber/20-gcc/dat/slko/3ob-3-1/Na-H.skf
| 5 2 (C ) 1 (Na) /appl/soft/chem/amber/20-gcc/dat/slko/3ob-3-1/C-Na.skf
| 6 2 (C ) 2 (C ) /appl/soft/chem/amber/20-gcc/dat/slko/3ob-3-1/C-C.skf
| 7 2 (C ) 3 (O ) /appl/soft/chem/amber/20-gcc/dat/slko/3ob-3-1/C-O.skf
| 8 2 (C ) 4 (H ) /appl/soft/chem/amber/20-gcc/dat/slko/3ob-3-1/C-H.skf
| 9 3 (O ) 1 (Na) /appl/soft/chem/amber/20-gcc/dat/slko/3ob-3-1/O-Na.skf
| 10 3 (O ) 2 (C ) /appl/soft/chem/amber/20-gcc/dat/slko/3ob-3-1/O-C.skf
| 11 3 (O ) 3 (O ) /appl/soft/chem/amber/20-gcc/dat/slko/3ob-3-1/O-O.skf
| 12 3 (O ) 4 (H ) /appl/soft/chem/amber/20-gcc/dat/slko/3ob-3-1/O-H.skf
| 13 4 (H ) 1 (Na) /appl/soft/chem/amber/20-gcc/dat/slko/3ob-3-1/H-Na.skf
| 14 4 (H ) 2 (C ) /appl/soft/chem/amber/20-gcc/dat/slko/3ob-3-1/H-C.skf
| 15 4 (H ) 3 (O ) /appl/soft/chem/amber/20-gcc/dat/slko/3ob-3-1/H-O.skf
| 16 4 (H ) 4 (H ) /appl/soft/chem/amber/20-gcc/dat/slko/3ob-3-1/H-H.skf
SANDER BOMB in subroutine qm2_dftb_get_dftb3_parameters
Hubbard derivative dU/dq not found.
Element Na not supported.
I tried to use amber/18, amber/20, amber/20_new but regardless of the version I seem to have the same problem.
I also have ended up downloading all the files from
https://dftb.org/parameters/download/all-sk-files just in case something was missing. The results are the same. Is there a straightforward way to solve this?
The input file looks like this:
Acet, meoh: 300ps MD, No constraints, now with constant volume, keeping thermal bath
&cntrl
imin = 0, ! do MD (no minimization)
irest = 0, ! restart calculation
ntx = 1, ! no vel
ntb = 0, ! NON-PERIODIC
ntp = 0, ! 0) No pressure scaling 1) constant pressure dynamics, isotropic position scaling
tautp = 10.0, ! Time constant, in ps, for heat bath coupling for the system, if ntt = 1.
cut = 9.0, ! force cutoff boundary
ntr = 0, ! NO Position restraints
NTC = 1, ! SHAKE not performed
NTF = 1, ! complete interaction is calculated (default)
jfastw=4 ! No shake mask
tempi = 295.15, ! intial temp
temp0 = 295.15, ! goal, final temp
ntt = 1, ! Use Langevin dynamics using the weak-coupling algorithm, see tautp
ig=-1, ! random seed will be based on the current date and time
nstlim = 3,! the number of MD steps
dt = 0.001, ! time step (ps)
ntpr = 1, ! results prited every ntpr
ntwx = 1, ! coordinate file printed every ntwx
ntwr = 1, ! restart file printed every ntwr
ifqnt = 1, ! Flag for QM/MM run
/
&qmmm
qmmask=':9,53,47,51,26,118,86,70,126,132,135-154', ! QM treated
qmcharge =0, ! Charge of QM region
qm_theory ='DFTB3',! Use PM3 Hamiltonian (default)
qm_ewald=0, ! Use Ewald type treatment for long range Electrostatics
qm_pme=1 ! Particle Mesh Ewald method
Thanks,
Pau
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Received on Thu Mar 17 2022 - 03:00:02 PDT
