Hello,
I built a single layer of graphite according to the crystal operation.
And I tried to generate the parameter file for it with antechamber.
When I run antechamber as following, I got this error.
antechamber -fi pdb -fo mol2 -i grap2.pdb -o grap2.mol2
-------------------------------------------------------------------
The atom number exceeds the MAXATOM, reallocate memory
Info: the bond number exceeds MAXBOND, reallocate memory automatically
Info: the atom number exceeds the MAXATOM, reallocate memory automatically
Info: the actual number of rings (72588) exceeds the defaut ring size
(500), reallocate memory automatically
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/bkim/packages/amber11/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit
------------------------------------------------------------
I attached the input pdb file of graphite.
If you have any idea to avoid this error, please let me know.
Thank you.
Bongkeun Kim
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Received on Thu Oct 14 2010 - 13:30:04 PDT
