Thank you, Adrian! Actually, this stems from a previous step where I use
pdb4amber to post-process a protein-ligand complex PDB file. According to
the PDB file format, columns 77-78 must contain the element symbol ('Br').
https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#HETATM
However, pdb4amber places only the first character ('B') in column 78, thus
the program that generates sqm input reads it as Boron. I am attaching a
sample PDB file where I corrected the column format but pdb4amber still
changes it. To reproduce it do:
pdb4amber -i input.pdb -o input_tmp.pdb --add-missing-atoms -l input_tmp.log
Best,
Thomas
On Sat, 26 Jun 2021 at 21:13, Roitberg,Adrian E <roitberg.ufl.edu> wrote:
> 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
> of Sciences <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.uochb.cz_web_structure_31.html-3Flang-3Den&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=g0ss3ChSklkGbp0HjEn1rKyf08EthoNWyZAxtdd7I74&s=fDb09939UPS3r3lIGTkaBfB8cBPl2JhD47CNDNCV1_8&e=
> >, Prague,
> Czech Republic
> &
> CEITEC - Central European Institute of Technology
> <
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--
======================================================================
Dr. Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague,
Czech Republic
&
CEITEC - Central European Institute of Technology
<https://www.ceitec.eu/>, Brno,
Czech Republic
email: tevang3.gmail.com, Twitter: tevangelidis
<https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis
<https://www.linkedin.com/in/thomas-evangelidis-495b45125/>
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Mon Jun 28 2021 - 06:00:02 PDT
