Just focus on 'Br' of the ligand in the attached PDB file. The
single-letter elements must be right-justified while (by mistake) I have
them left-justified.
Thomas
On Mon, 28 Jun 2021 at 14:29, Thomas Evangelidis <tevang3.gmail.com> wrote:
> 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
>> <
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ceitec.eu_&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=g0ss3ChSklkGbp0HjEn1rKyf08EthoNWyZAxtdd7I74&s=irYThYPW2NC88re9P__ijAx9BvCdhkCOOYmkDXg4_AU&e=
>> >, Brno,
>> Czech Republic
>>
>> email: tevang3.gmail.com, Twitter: tevangelidis
>> <
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_tevangelidis&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=g0ss3ChSklkGbp0HjEn1rKyf08EthoNWyZAxtdd7I74&s=LwdJKZlO-vh4gTIgApcGaoDsS5F6gRZGtZDQOYnA6-c&e=
>> >, LinkedIn: Thomas Evangelidis
>> <
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_in_thomas-2Devangelidis-2D495b45125_&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=g0ss3ChSklkGbp0HjEn1rKyf08EthoNWyZAxtdd7I74&s=PhtP2bAD_GFvd600ocrT9Bm9HxFPDpN3kUAY-v4mo6E&e=
>> >
>>
>> website:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__sites.google.com_site_thomasevangelidishomepage_&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=g0ss3ChSklkGbp0HjEn1rKyf08EthoNWyZAxtdd7I74&s=EbNRTF_4BOL0_fmx0p3se5V7b_Z7T43GPFAfOjtaYfs&e=
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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/
>
>
>
>
--
======================================================================
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 - 06:00:03 PDT
