Dear Hafiz,
In case this is still relevant:
The trans3d parameters are not DFTB3 parameters. They are DFTB2 (=SCC-DFTB) parameters that have to be used in conjunction with the mio-1-1 parameters. Please try to add the Slater-Koster files to the folder with the mio-1-1 parameters, and then choose DFTB2 as method.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
> On Dec 3, 2020, at 3:04 PM, Hafiz Saqib Ali <hafizsaqib.ali.manchester.ac.uk> wrote:
>
> 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://urldefense.com/v3/__https://dftb.org/parameters/download__;!!Mih3wA!T8Iet8K2itq7GtC0T3ftYX69x5RxvyDwxNAUI8x1pTI0p00VyAsFQjWduHmoC80$ ) 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 Tue Jan 12 2021 - 16:30:02 PST
