Hello,
I am working on protonated sugars and their binding energies.
Therefore, some of my work involve transition state and reactive
intermediate modelling. However, I've been encountering a problem when
bond distance is less than 1.9A between a C and an O atom (i.e, 1.8A
fails to do the resp fitting or AM1-BCC). The error goes similar to
this:
For atom[x]:O5, the best APS is not zero, bonds involved by this atom
are frozen
The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8
(aromatic double)Error: cannot run
"/usr/local/Amber10/amber10/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit
Obviously, antechamber does not recognize the triply bonded oxygen at
such a distance, but this precludes me from doing the charge generation.
If I don't have the correct charges, I cannot proceed to the step in
which I create the parameters, which I can tailor according to my needs.
Is there any way to overcome this problem?
Thanks,
Alican
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Received on Tue Aug 26 2014 - 15:30:02 PDT
