Dear Amber Community,
I am running QM/MM MD simulation of a reaction catalysed by a non-heme iron enzyme via umbrella sampling technique. For this purpose I have used DFTB3 method for QM region and I have downloaded these DFTB3 parameters (trans3d) from DFTB (
https://dftb.org/parameters/download) and paste it in the AMBER directory. When I try to run QM/MM simulation, AMBER recognised DFTB3 parameters for all atoms including Iron but I am getting following error:
I also attached my QM/MM-MD input file with this email.
I would be highly appreciated if someone help me to solve this problem.
Parameter files:
TYP (AT) TYP (AT) SK integral FILE
| 1 1 (N ) 1 (N ) /home/hafiz/amber16/dat/slko/3ob-3-1/N-N.skf
| 2 1 (N ) 2 (H ) /home/hafiz/amber16/dat/slko/3ob-3-1/N-H.skf
| 3 1 (N ) 3 (C ) /home/hafiz/amber16/dat/slko/3ob-3-1/N-C.skf
| 4 1 (N ) 4 (O ) /home/hafiz/amber16/dat/slko/3ob-3-1/N-O.skf
| 5 1 (N ) 5 (Fe) /home/hafiz/amber16/dat/slko/3ob-3-1/N-Fe.skf
| 6 2 (H ) 1 (N ) /home/hafiz/amber16/dat/slko/3ob-3-1/H-N.skf
| 7 2 (H ) 2 (H ) /home/hafiz/amber16/dat/slko/3ob-3-1/H-H.skf
| 8 2 (H ) 3 (C ) /home/hafiz/amber16/dat/slko/3ob-3-1/H-C.skf
| 9 2 (H ) 4 (O ) /home/hafiz/amber16/dat/slko/3ob-3-1/H-O.skf
| 10 2 (H ) 5 (Fe) /home/hafiz/amber16/dat/slko/3ob-3-1/H-Fe.skf
| 11 3 (C ) 1 (N ) /home/hafiz/amber16/dat/slko/3ob-3-1/C-N.skf
| 12 3 (C ) 2 (H ) /home/hafiz/amber16/dat/slko/3ob-3-1/C-H.skf
| 13 3 (C ) 3 (C ) /home/hafiz/amber16/dat/slko/3ob-3-1/C-C.skf
| 14 3 (C ) 4 (O ) /home/hafiz/amber16/dat/slko/3ob-3-1/C-O.skf
| 15 3 (C ) 5 (Fe) /home/hafiz/amber16/dat/slko/3ob-3-1/C-Fe.skf
| 16 4 (O ) 1 (N ) /home/hafiz/amber16/dat/slko/3ob-3-1/O-N.skf
| 17 4 (O ) 2 (H ) /home/hafiz/amber16/dat/slko/3ob-3-1/O-H.skf
| 18 4 (O ) 3 (C ) /home/hafiz/amber16/dat/slko/3ob-3-1/O-C.skf
| 19 4 (O ) 4 (O ) /home/hafiz/amber16/dat/slko/3ob-3-1/O-O.skf
| 20 4 (O ) 5 (Fe) /home/hafiz/amber16/dat/slko/3ob-3-1/O-Fe.skf
| 21 5 (Fe) 1 (N ) /home/hafiz/amber16/dat/slko/3ob-3-1/Fe-N.skf
| 22 5 (Fe) 2 (H ) /home/hafiz/amber16/dat/slko/3ob-3-1/Fe-H.skf
| 23 5 (Fe) 3 (C ) /home/hafiz/amber16/dat/slko/3ob-3-1/Fe-C.skf
| 24 5 (Fe) 4 (O ) /home/hafiz/amber16/dat/slko/3ob-3-1/Fe-O.skf
| 25 5 (Fe) 5 (Fe) /home/hafiz/amber16/dat/slko/3ob-3-1/Fe-Fe.skf
SANDER BOMB in subroutine qm2_dftb_get_dftb3_parameters
Hubbard derivative dU/dq not found.
Element Fe not supported.
Thanks
Hafiz
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Received on Thu Dec 03 2020 - 15:30:02 PST
