Hello AMBER,
I got a segmentation fault error when I used antechamber and parmchk
command to generate prep file for carbon nanotube.
This was successful for short CNT about 1~2nm long.
But the error occurred when trying 4 and 5nm long CNT.
I did two different way.
1. simply assign cm2 charge from anechamber
antechamber -fi mol2 -fo prepi -i ACDOCTOR.mol2 -o cnt884.prepi -c cm2 -rn CNT
output is simply
Segmentation fault
2. use acdoctor
2-1 use acdoctor to validate input
acdoctor -i cnt884.pdb -f pdb
2-2 use prepgen to have prepi file
prepgen -i ACDOCTOR_ATOM.ac -o cnt884.prepi -rn CNT
2-3 parmchk for additional frcmod file
parmchk -i cnt884.prepi -o cnt884.frcmod -f prepi
The final output from parmchk was
---------------------------------------
Info: the atom number exceeds the MAXATOM, reallocate memory automatically
Info: the atom number exceeds the MAXATOM, reallocate memory automatically
Info: the atom number exceeds the MAXATOM, reallocate memory automatically
Info: the atom number exceeds the MAXATOM, reallocate memory automatically
Info: the atom number exceeds the MAXATOM, reallocate memory automatically
Segmentation fault
---------------------------------------------
I attached my input files. Please let me know what causes this problem.
Thank you.
Bongkeun Kim
bkim at chem.ucsb.edu
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Received on Mon Apr 11 2011 - 13:30:02 PDT
