Good to hear. Hopefully this is helpful to others trying to do a similar
task. Building CNTs (and related structures) with leap is not easy, since I
don't think that was in its list of target applications when it was
designed. It takes clever maneuvering to get leap to do what you want with
those systems.
All the best,
Jason
On Mon, Apr 11, 2011 at 2:06 PM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
> Hello Jason,
>
> I just extracted only 160 atoms and generated prepi file without problem.
> Then I separated a big CNT with residues based on the index every 160
> atoms.
> Finally I used bondByDistance command in tleap to connect residues with
> bonds.
> All things were successful.
> Thank you.
> Bongkeun Kim
>
> Quoting Jason Swails <jason.swails.gmail.com>:
>
> > 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
> >
>
>
>
>
>
> _______________________________________________
> 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
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Received on Mon Apr 11 2011 - 15:00:02 PDT
