AMBER Archive (2003)

Subject: how to set up a carbon nanotube pdb file

From: zhaoxc_at_puccini.che.pitt.edu
Date: Mon May 05 2003 - 16:24:10 CDT

Hi,

I am using AMBER 7 to simulate a carbon nanotube. The nanotube has 576
carbon atoms. I want to use the potential parameters of "CA" in parm99
for each C atom in the nanotube. I generated the pdb file by BABEL, it
looks like

ATOM 1 C UNK 1 5.239 1.404 0.000 1.00 0.00
ATOM 2 C UNK 1 5.378 0.708 1.230 1.00 0.00
ATOM 3 C UNK 1 4.303 3.302 1.230 1.00 0.00
ATOM 4 C UNK 1 4.697 2.712 2.460 1.00 0.00
ATOM 5 C UNK 1 2.712 4.697 0.000 1.00 0.00
ATOM 6 C UNK 1 3.302 4.303 1.230 1.00 0.00
ATOM 7 C UNK 1 0.708 5.378 1.230 1.00 0.00
ATOM 8 C UNK 1 1.404 5.239 2.460 1.00 0.00
ATOM 9 C UNK 1 -1.404 5.239 0.000 1.00 0.00
ATOM 10 C UNK 1 -0.708 5.378 1.230 1.00 0.00
ATOM 11 C UNK 1 -3.302 4.303 1.230 1.00 0.00
........

with the necessary connection info. Can you suggest an easy way to modify
this pdb file so that leap can recognize the residue and load in the
correct potential parameters?

Thanks

Xiongce Zhao 

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