Hi There,
I want to simulate carbon nanotubes (CNT) with implicit water, so I need to
translate the topology from Gromacs format to Amber format.
I tried antechamber using the pdb file, planning to manually modify the
parameters after the file is constructed. However my tube is big (1200
carbon atoms), and antechamber said "The atom number exceeds the MAXATOM,
reallocate memory", and eventually crashed.
I also think of divide the long tube into small ones, but it seems that I
need to manually add the bond/angle/dihydral to connect the small tubes. The
number of connections seems to be quite large, and I am not quite know of
how to add it. So I still look for a better way of doing it.
May I have advice on this issue? Thanks!
--
Yan Gao
Jacobs School of Engineering
University of California, San Diego
Tel: 858-952-2308
Email: Yan.Gao.2001.gmail.com
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Received on Thu Jul 08 2010 - 14:00:05 PDT
