Hi everyone,
I am trying to create an acetic acid molecule with xleap and generate a pdb
and mol2 file. I am able to create the molecule in xleap. However, I am not
able to add the double bond between the C and O. The resulting pdb file
generated is:
ATOM 1 C1 aaa 1 12.735 -2.914 0.000 1.00
0.00
ATOM 2 C2 aaa 1 11.238 -3.020 0.000 1.00 0.00
ATOM 3 H4 aaa 1 12.805 -3.912 0.000 1.00 0.00
ATOM 4 H5 aaa 1 13.590 -3.432 0.000 1.00 0.00
ATOM 5 H6 aaa 1 13.253 -2.059 0.000 1.00 0.00
ATOM 6 O7 aaa 1 11.776 -4.420 0.000 1.00 0.00
ATOM 7 O8 aaa 1 10.057 -3.945 0.000 1.00 0.00
ATOM 8 H9 aaa 1 9.213 -3.408 0.000 1.00 0.00
TER
END
When I try to generate the mol2 file with antechamber:
antechamber -i AAA.pdb -fi pdb -o AAA.mol2 -fo mol2 -c bcc -nc 0
I receive the following error because the number of atoms and bonds do not
make sense when the double bond is not included.
For atom[6]:O7, the best APS is not zero, bonds involved by this atom are
frozen
For atom[7]:O8, 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
"/opt/software/Amber/14Tools15--Intel-13.0.1.117/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit
My question is, how can I make one of the bonds in xleap a double bond
and/or generate a mol2 file that I can subsequently alter.
Thank you very much!
--
Aseel Bala Ahmed
Michigan State University
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Received on Wed Feb 15 2017 - 11:30:02 PST
