Dear All,
I am using Amber22 and wish to perform equilibration under QM/MM regime. Right after the job starts there’s an error:
&&&&&&&&&&&&&
Parameter files:
TYP (AT) TYP (AT) SK integral FILE
| 1 1 (S ) 1 (S ) /net/software/testing/software/Amber/22.1-intel-2021b-AmberTools-22.3-updated-cpptraj/dat/slko/mio-1-1/S-S.skf
| 2 1 (S ) 2 (C ) /net/software/testing/software/Amber/22.1-intel-2021b-AmberTools-22.3-updated-cpptraj/dat/slko/mio-1-1/S-C.skf
| 3 1 (S ) 3 (H ) /net/software/testing/software/Amber/22.1-intel-2021b-AmberTools-22.3-updated-cpptraj/dat/slko/mio-1-1/S-H.skf
| 4 1 (S ) 4 (O ) /net/software/testing/software/Amber/22.1-intel-2021b-AmberTools-22.3-updated-cpptraj/dat/slko/mio-1-1/S-O.skf
| 5 1 (S ) 5 (N ) /net/software/testing/software/Amber/22.1-intel-2021b-AmberTools-22.3-updated-cpptraj/dat/slko/mio-1-1/S-N.skf
| 6 1 (S ) 6 () /net/software/testing/software/Amber/22.1-intel-2021b-AmberTools-22.3-updated-cpptraj/dat/slko/mio-1-1/S-.skf
****************************************************
* !! A FILE NEEDED BY DFTB WAS NOT FOUND !! *
****************************************************
Missing file:
/net/software/testing/software/Amber/22.1-intel-2021b-AmberTools-22.3-updated-c
pptraj/dat/slko/mio-1-1/S-.skf
[...]
SANDER BOMB in subroutine qm2_dftb_check_slko_file <qm2_dftb_load_params.f>
File not found.
Exiting.
&&&&&&&&&&&&&
The guys at HPC have told me the files are present but actuallyI think the issue is seeks for the empty atom type (?):
&&&&&&&&&&&&&
| 6 1 (S ) 6 () /net/software/testing/software/Amber/22.1-intel-2021b-AmberTools-22.3-updated-cpptraj/dat/slko/mio-1-1/S-.skf
&&&&&&&&&&&&&
I wonder what is going on. The input file is:
&&&&&&&&&&&&&
Equilibration
&cntrl
dt=0.001, ! time-step [fs] (1 fs) {1 fs = 0.001 ps}
nstlim=50000, ! steps (50.000 steps) {50 ps = 0.001 ps * 50.000 steps}
taup=1, ! pressure relaxation time (1 ps)
ntc=2, ! SHAKE for bonds involving hydrogen are constrained
cut=8.0, ! direct-space cut-off of 8A for non-bonded interaction with PME for long-range electrostatics
ifqnt=1, ! turn-on QMMM
/
&qmmm
qmmask='.2135-2140 | :275 | .702-705 | @670-697',
qm_theory='SCC-DFTB',
qmcharge=-2,
/
&&&&&&&&&&&&&
For the QM region and atom types assigned please take a look here: https://imgur.com/a/Caz8CVi <https://imgur.com/a/Caz8CVi>
Appreciate help!
Sincerely,
Maciej
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Received on Fri Feb 17 2023 - 01:00:02 PST
