Dear Amber users
I am trying to use antechamber to generate GAFF parameters for simulation of C60 clusters. However, I found the following error:
I key in
$AMBERHOME/bin/antechamber -i fullerene2.pdb -fi pdb -o fullerene.mol2 -fo mol2 -c bcc
and get
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 computation time
Error: cannot run "/home/cwpao/amber11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit
Enclosed is the PDB file of the C60. Could anyone tell me what happened? I suspect that this is due to the pentagon C atoms.
Thanks!
C.W.
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Received on Mon Mar 22 2010 - 21:00:04 PDT
