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.
>
>
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Received on Tue Sep 13 2016 - 04:30:03 PDT
