Hello,
I am trying to create parameters for a quite big organic molecule (212 atoms). I have used the Antechamber protocol to obtain the .top and .crd for smaller molecules many times, and everything was OK, but now I am receiving a Segment Violitation (Core) in the step of parmchk. I have used the option -l 9 in the steps respgen. This is what I done, the step where I get Segment Violation errors is the last one:
$AMBERHOME/exe/espgen -i lanzar_SP.sh.o4732912 -o cargas.esp
$AMBERHOME/exe/antechamber -i monomero_fullereno.mol2 -fi mol2 -o minimizado.ac -fo ac
$AMBERHOME/exe/respgen -i minimizado.ac -o minimizado.respin1 -f resp1 -l 9
$AMBERHOME/exe/respgen -i minimizado.ac -o minimizado.respin2 -f resp2 -l 9
$AMBERHOME/exe/resp -i minimizado.respin1 -o minimizado.respout1 -e cargas.esp -t qout_1 -O
$AMBERHOME/exe/resp -i minimizado.respin2 -o minimizado.respout2 -e cargas.esp -t qout_2 -q qout_1 -O
$AMBERHOME/exe/antechamber -i minimizado.ac -fi ac -o minimizado_resp.mol2 -fo mol2 -c rc -cf qout_2
$AMBERHOME/exe/antechamber -fi mol2 -i minimizado_resp.mol2 -c rc -cf qout_2 -fo ac -o minimizado_resp.ac
$AMBERHOME/exe/atomtype -i minimizado_resp.ac -o minimizado_resp_gaff.ac -p gaff
$AMBERHOME/exe/prepgen -i minimizado_resp_gaff.ac -o minimizado_resp_gaff.prepc -f car
$AMBERHOME/exe/parmchk -i minimizado_resp_gaff.prepc -o minimizado.frcmod -f prepc
Could you please help me to solve this problem? How could I get the .frcmod file for my 212 atoms- system?
Thanks a lot in advance.
Best wishes,
Rebeca.
Dr. Rebeca Garcia
Santiago de Compostela University
Spain
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Received on Tue May 21 2013 - 05:30:03 PDT
