AMBER Archive (2009)

Subject: Re: [AMBER] problem with parmchk

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon May 18 2009 - 15:00:07 CDT

On Mon, May 18, 2009, rebeca wrote:

> thanks for your answer. Actually, the system has only 264 rings, I donīt
> know why antechamber thinks that it has 8616. The number of atoms is 312.
> It is a carbon nanotube, consisting only in aromatic six member rings
> joined to each other.

I think, as you have discovered, that antechamber won't help much in
parameterizing this system. It is designed for drug-like molecules, and is
not set up to handle a system like this.

On the other hand, you have only a small number of atom types, and a by-hand
approach is certainly possible, depending on what you want to learn. Try a
Google search on "carbon nanotube force field" (or similar) to see what others
have done in this area.

...dac

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