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 - 04:30:02 PDT
