Hello Shahab,
Thankfully, SQM has already identified the problem:
" UNSUPPORTED ELEMENT"
It has flagged atom 28 as the culprit, and if you look at this atom in your
PDB, the atom type is "Xx". Last time I checked, "Xx" wasn't on the
periodic table! If you correct that, then this error *should* be resolved,
I believe.
Take care,
Sam
On Tue, Sep 13, 2016 at 6:31 AM, shahab shariati <shahab.shariati.gmail.com>
wrote:
> the PDB file of my ligand (Doxorubicin) is as follows:
>
> HETATM 2259 N LIG 1 48.790 23.456 22.737 1.00 0.00
> N
> HETATM 2260 C LIG 1 47.677 21.976 25.428 1.00 0.00
> C
> HETATM 2261 C LIG 1 47.239 26.983 24.996 1.00 0.00
> C
> HETATM 2262 C LIG 1 45.079 26.200 25.865 1.00 0.00
> C
> HETATM 2263 C LIG 1 50.227 24.708 24.308 1.00 0.00
> C
> HETATM 2264 C LIG 1 45.744 27.368 25.078 1.00 0.00
> C
> HETATM 2265 C LIG 1 49.173 22.318 25.691 1.00 0.00
> C
> HETATM 2266 C LIG 1 47.927 26.730 26.374 1.00 0.00
> C
> HETATM 2267 C LIG 1 50.117 22.176 24.455 1.00 0.00
> C
> HETATM 2268 C LIG 1 45.548 28.750 25.544 1.00 0.00
> C
> HETATM 2269 C LIG 1 44.547 24.801 30.653 1.00 0.00
> C
> HETATM 2270 C LIG 1 47.273 25.109 31.099 1.00 0.00
> C
> HETATM 2271 C LIG 1 48.477 25.868 34.784 1.00 0.00
> C
> HETATM 2272 C LIG 1 46.482 29.556 26.306 1.00 0.00
> C
> HETATM 2273 C LIG 1 50.050 23.399 23.501 1.00 0.00
> C
> HETATM 2274 C LIG 1 49.205 24.774 25.478 1.00 0.00
> C
> HETATM 2275 O LIG 1 43.342 24.648 30.490 1.00 0.00
> O
> HETATM 2276 O LIG 1 48.487 25.079 31.278 1.00 0.00
> O
> HETATM 2277 O LIG 1 44.491 29.303 25.258 1.00 0.00
> O
> HETATM 2278 O LIG 1 49.201 26.039 26.186 1.00 0.00
> O
> HETATM 2279 O LIG 1 49.367 23.613 26.327 1.00 0.00
> O
> HETATM 2280 O LIG 1 48.113 24.946 33.885 1.00 0.00
> O
> HETATM 2281 O LIG 1 48.811 26.070 28.945 1.00 0.00
> O
> HETATM 2282 O LIG 1 43.650 25.144 28.013 1.00 0.00
> O
> HETATM 2283 O LIG 1 45.238 27.320 23.740 1.00 0.00
> O
> HETATM 2284 O LIG 1 49.918 20.967 23.726 1.00 0.00
> O
> HETATM 2285 O LIG 1 46.084 29.601 27.671 1.00 0.00
> O
> HETATM 2286 C LIG 1 44.708 24.031 34.319 1.00 0.00
> Xx
> HETATM 2287 C LIG 1 45.674 25.896 27.207 1.00 0.00
> Xx
> HETATM 2288 C LIG 1 47.059 26.121 27.440 1.00 0.00
> Xx
> HETATM 2289 C LIG 1 44.208 24.231 33.026 1.00 0.00
> Xx
> HETATM 2290 C LIG 1 45.053 24.609 31.947 1.00 0.00
> Xx
> HETATM 2291 C LIG 1 46.067 24.250 34.572 1.00 0.00
> Xx
> HETATM 2292 C LIG 1 46.445 24.802 32.195 1.00 0.00
> Xx
> HETATM 2293 C LIG 1 46.768 25.384 29.807 1.00 0.00
> Xx
> HETATM 2294 C LIG 1 45.372 25.189 29.572 1.00 0.00
> Xx
> HETATM 2295 C LIG 1 46.922 24.674 33.535 1.00 0.00
> Xx
> HETATM 2296 C LIG 1 44.863 25.402 28.258 1.00 0.00
> Xx
> HETATM 2297 C LIG 1 47.582 25.852 28.733 1.00 0.00
> Xx
> HETATM 2298 H LIG 1 46.258 28.699 28.013 1.00 0.00
> H
> HETATM 2299 H LIG 1 50.520 21.030 22.956 1.00 0.00
> H
> HETATM 2300 H LIG 1 44.430 26.768 23.775 1.00 0.00
> H
> HETATM 2301 H LIG 1 49.426 25.445 28.900 1.00 0.00
> H
> HETATM 2302 H LIG 1 43.216 25.477 27.327 1.00 0.00
> H
> HETATM 2303 H LIG 1 48.871 24.208 22.049 1.00 0.00
> H
> HETATM 2304 H LIG 1 48.683 22.579 22.225 1.00 0.00
> H
> HETATM 2305 H01 LIG 1 46.465 24.092 35.574 1.00 0.00
> H
> HETATM 2306 H02 LIG 1 47.299 21.351 26.237 1.00 0.00
> H
> HETATM 2307 H03 LIG 1 47.771 27.791 24.494 1.00 0.00
> H
> HETATM 2308 H04 LIG 1 45.152 25.300 25.254 1.00 0.00
> H
> HETATM 2309 H05 LIG 1 50.071 25.561 23.647 1.00 0.00
> H
> HETATM 2310 H06 LIG 1 49.473 21.541 26.394 1.00 0.00
> H
> HETATM 2311 H07 LIG 1 48.129 27.717 26.791 1.00 0.00
> H
> HETATM 2312 H08 LIG 1 51.120 22.137 24.881 1.00 0.00
> H
> HETATM 2313 H09 LIG 1 48.712 25.381 35.730 1.00 0.00
> H
> HETATM 2314 H10 LIG 1 46.501 30.568 25.901 1.00 0.00
> H
> HETATM 2315 H11 LIG 1 50.861 23.287 22.782 1.00 0.00
> H
> HETATM 2316 H12 LIG 1 48.201 24.737 25.055 1.00 0.00
> H
> HETATM 2317 H13 LIG 1 44.045 23.708 35.121 1.00 0.00
> H
> HETATM 2318 H14 LIG 1 43.143 24.093 32.842 1.00 0.00
> H
> HETATM 2319 H15 LIG 1 47.476 29.113 26.237 1.00 0.00
> H
> HETATM 2320 H16 LIG 1 47.587 21.441 24.482 1.00 0.00
> H
> HETATM 2321 H17 LIG 1 47.283 26.038 24.454 1.00 0.00
> H
> HETATM 2322 H18 LIG 1 44.056 26.520 26.061 1.00 0.00
> H
> HETATM 2323 H19 LIG 1 51.235 24.731 24.722 1.00 0.00
> H
> HETATM 2324 H20 LIG 1 47.661 26.575 34.931 1.00 0.00
> H
> HETATM 2325 H21 LIG 1 49.357 26.400 34.422 1.00 0.00
> H
> HETATM 2326 H22 LIG 1 47.097 22.898 25.381 1.00 0.00
> H
>
> On Tue, Sep 13, 2016 at 3:58 PM, shahab shariati <
> shahab.shariati.gmail.com>
> wrote:
>
> > sqm.out file is as follows:
> >
> > --------------------------------------------------------
> > AMBER SQM VERSION 14
> >
> > By
> > Ross C. Walker, Michael F. Crowley, Scott Brozell,
> > Tim Giese, Andreas W. Goetz,
> > Tai-Sung Lee and David A. Case
> >
> > --------------------------------------------------------
> >
> >
> > ------------------------------------------------------------
> > --------------------
> > QM CALCULATION INFO
> > ------------------------------------------------------------
> > --------------------
> > QMMM: Atom number: 28 has atomic number 0.
> > QMMM: There are no AM1 parameters for this element. Sorry.
> > SANDER BOMB in subroutine qm2_load_params_and_allocate
> > UNSUPPORTED ELEMENT
> > QM AM1 NOT AVAILABLE FOR THIS ATOM
> > ~
> >
> >
> > On Tue, Sep 13, 2016 at 3:55 PM, shahab shariati <
> > shahab.shariati.gmail.com> wrote:
> >
> >> Dear amber users,
> >>
> >> I am using antechamber for my ligand (Doxorubicin).
> >>
> >> I have encountered with error:
> >>
> >>
> >> $AMBERHOME/bin/antechamber -i dox.pdb -fi pdb -o dox.mol2 -fo mol2 -c
> bcc
> >> -s 2
> >>
> >> Running: /share/apps/amber/amber14/bin/bondtype -j full -i
> >> ANTECHAMBER_BOND_TYPE.AC0 -o ANTE
> >> CHAMBER_BOND_TYPE.AC -f ac
> >>
> >> For atom[28]:Xx, the best APS is not zero, bonds involved by this atom
> >> are frozen
> >>
> >> For atom[29]:Xx, the best APS is not zero, bonds involved by this atom
> >> are frozen
> >>
> >> For atom[30]:Xx, the best APS is not zero, bonds involved by this atom
> >> are frozen
> >>
> >> For atom[31]:Xx, the best APS is not zero, bonds involved by this atom
> >> are frozen
> >>
> >> For atom[32]:Xx, the best APS is not zero, bonds involved by this atom
> >> are frozen
> >>
> >> For atom[33]:Xx, the best APS is not zero, bonds involved by this atom
> >> are frozen
> >>
> >> For atom[34]:Xx, the best APS is not zero, bonds involved by this atom
> >> are frozen
> >>
> >> For atom[35]:Xx, the best APS is not zero, bonds involved by this atom
> >> are frozen
> >>
> >> For atom[36]:Xx, the best APS is not zero, bonds involved by this atom
> >> are frozen
> >>
> >> For atom[37]:Xx, the best APS is not zero, bonds involved by this atom
> >> are frozen
> >>
> >> For atom[38]:Xx, the best APS is not zero, bonds involved by this atom
> >> are frozen
> >>
> >> For atom[39]:Xx, the best APS is not zero, bonds involved by this atom
> >> are frozen
> >>
> >> Warning: the assigned bond types may be wrong, please :
> >> (1) double check the structure (the connectivity) and/or
> >> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> >> (3) increase PSCUTOFF in define.h and recompile bondtype.c
> >> Be cautious, use a large value of PSCUTOFF (>100) will significantly
> >> increase the computat ion time
> >>
> >> Running: /share/apps/amber/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0
> -o
> >> ANTECHAMBER_AC.AC -p gaff
> >> Total number of electrons: 214; net charge: 0
> >>
> >> Running: /share/apps/amber/amber14/bin/sqm -O -i sqm.in -o sqm.out
> >> Error: cannot run "/share/apps/amber/amber14/bin/sqm -O -i sqm.in -o
> >> sqm.out" of bcc() in charge.c properly, exit
> >>
> >> I am beginner in amber. Please guide me to resolve this issue.
> >>
> >> Any help will highly appreciated.
> >>
> >>
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 13 2016 - 11:30:03 PDT
