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
>>
>>
>> _______________________________________________
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>>
>>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
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Received on Mon Apr 11 2011 - 14:30:03 PDT
