Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Thu, 8 Jul 2010 14:28:25 -0700

> 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.

You will need bond, angle and dihedral parameters whether the
molecule is one residue or many. But specifying the many
connections between multiple smaller residues could be a chore.
You might want to write a program to generate the leap cmds
to do this. It might also be tricky to turn a 1-residue pdb
into a multi-residue pdb; if the 1-res pdb was generated by
a program, you may want to modify that program.

Given all that, it may be worth trying to debug antechamber
to allow the 1-res version.


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Received on Thu Jul 08 2010 - 14:30:05 PDT
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