Dear all:
Using Gaussian03 we have optimized a Modified uridine base (2'methoxy
4'aminomethyl) with DFT method. Using the optmized output geometry We
calculated the ESP charge for each atom. The output was looking quite good
while viewing with Gaussview, then using antechamber I tried to convert the
output in to mol2 file with the ESP charge on each atom by following command
$AMBERHOME/exe/antechamber -i uridine.log -fi gout -o uridine.mol2 -fo mol2
-c resp
but it fails to convert the output in to mol2 file
Error was:
For atom[5]:O2, 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 "/home/ppilab/sudhi/amber10/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit
Could anybody suggest some solution for this
S.Harikrishna
Junior Research fellow
Dept of Chemistry
Indian Institute of Technology Bombay
Mumbai - 400076
India
E-mail: krishna.s.iitb.ac.in
Mob: +91-8144802064
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Received on Sat Jun 11 2011 - 02:30:03 PDT
