Your coordinate section has an atomic number of 5 (which is boron), for the atom you claim is a Br. So the problem is not in SQM but in how you created those coordinates
On Jun 26, 2021 11:31 AM, Thomas Evangelidis <tevang3.gmail.com> wrote:
[External Email]
Could someone please explain to me why sqm seeks the Boron parameter file
instead of Bromine? Below is my input file:
Run semi-empirical minimization
> &qmmm
> qm_theory='DFTB3', maxcyc=0, tight_p_conv=1, dftb_maxiter=500, scfconv=
> 1.0d-11 qmcharge=-1,
> /
> 8 O -7.0760 -0.7300 25.4910
> 6 C -5.8230 -0.3700 26.0340
> 6 C1 -5.2210 0.8590 25.3200
> 6 C2 -3.9280 1.3390 26.0190
> 6 C3 -2.7140 0.4220 25.7330
> 7 N -2.4830 0.2320 24.2630
> 6 C4 -3.7080 -0.3050 23.5990
> 6 C5 -4.9300 0.6100 23.8190
> 6 C6 -1.2410 0.1710 23.6670
> 6 C7 -0.8480 0.5290 22.3580
> 5 Br -1.9150 1.2540 20.9940
> 7 N1 -0.2920 -0.3790 24.5010
> 6 C8 0.9630 -0.6360 24.0830
> 8 O1 1.7870 -1.1430 24.8340
> 7 N2 1.3780 -0.2800 22.7990
> 6 C9 0.4860 0.3300 21.9230
> 8 O2 0.9570 0.6670 20.8280
> 1 H 2.3370 -0.4530 22.5050
> 1 H1 -7.7790 -0.1250 25.8520
> 1 H2 -6.0150 -0.1690 27.1090
> 1 H3 -5.1770 -1.2720 25.9700
> 1 H4 -5.9770 1.6650 25.4010
> 1 H5 -3.6950 2.3660 25.6730
> 1 H6 -4.0880 1.4270 27.1140
> 1 H7 -1.8050 0.8580 26.2010
> 1 H8 -2.8450 -0.5730 26.2110
> 1 H9 -3.5190 -0.4570 22.5160
> 1 H10 -3.9090 -1.3230 23.9940
> 1 H11 -5.8190 0.1890 23.3060
> 1 H12 -4.7340 1.5830 23.3250
>
In the output file I get the following:
Parameter files:
> TYP (AT) TYP (AT) SK integral FILE
> | 1 1 (O ) 1 (O )
> /home1/evangel/Programs/amber20_src_static/dat/slko/3ob-3-1/O-O.skf
> | 2 1 (O ) 2 (C )
> /home1/evangel/Programs/amber20_src_static/dat/slko/3ob-3-1/O-C.skf
> | 3 1 (O ) 3 (N )
> /home1/evangel/Programs/amber20_src_static/dat/slko/3ob-3-1/O-N.skf
> | 4 1 (O ) 4 (B )
> /home1/evangel/Programs/amber20_src_static/dat/slko/3ob-3-1/O-B.skf
> ****************************************************
> * !! A FILE NEEDED BY DFTB WAS NOT FOUND !! *
> ****************************************************
>
> Missing file:
> /home1/evangel/Programs/amber20_src_static/dat/slko/3ob-3-1/O-B.skf
>
I guess the right file is
/home1/evangel/Programs/amber20_src_static/dat/slko/3ob-3-1/O-Br.skf, which
exists.
To reproduce it just run:
${AMBERHOME}/bin/sqm -O -i sqm.in -o sqm.out
>
--
======================================================================
Dr. Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
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&
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Received on Sat Jun 26 2021 - 12:30:02 PDT
