On Tue, May 21, 2013 at 8:29 AM, Rebeca García Fandiño
<regafan.hotmail.com>wrote:
> 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?
>
My suggestion is to use AmberTools13 (this appears to be Amber 9 or
something like that, given that $AMBERHOME/exe hasn't been a directory
we've used since about that time).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jun 14 2013 - 08:30:03 PDT
