Dear Amber users,
I am trying to create the parameter of a Carbon Nano Tube (CNT) using the antechamber.
I started with the making of the mol2 file for the CNT with the following command, however after more than 24 hours it hangs on like the following message.
The CNT has 576 atoms in total.
[user.compute-02]$ /usr/apps/amber11/AmberTools/bin/antechamber -i CNT.pdb -fi pdb -o CNT.mol2 -fo mol2 -c bcc -s 2
The atom number exceeds the MAXATOM, reallocate memory
Info: the bond number exceeds MAXBOND, reallocate memory automatically
Running: /usr/apps/amber11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Info: the atom number exceeds the MAXATOM, reallocate memory automatically
Info: the actual number of rings (17792) exceeds the defaut ring size (500), reallocate memory automatically
Running: /usr/apps/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: the atom number exceeds the MAXATOM, reallocate memory automatically
Info: the actual number of rings (17792) exceeds the defaut ring size (500), reallocate memory automatically
Total number of electrons: 3456; net charge: 0
Running: /usr/apps/amber11/bin/sqm -O -i sqm.in -o sqm.out
Please let me know your inputs on this and how to solve the issue.
Thanks
Jagur
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Received on Fri Aug 19 2011 - 10:00:04 PDT
