I'm guessing there's not enough memory to actually run these calculations.
Antechamber was meant for a smaller system (a single residue), and is not
really appropriate for treating entire CNTs. If you can break it up into
segments, and run antechamber/parmchk on those, then construct your large
CNT from these segments, you'll have a better chance of getting it to work.
HTH,
Jason
2011/4/11 Bongkeun Kim <bkim.chem.ucsb.edu>
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 11 2011 - 13:30:05 PDT
