AMBER Archive (2005)

Subject: Re: AMBER: How to make PDB file by myself

From: David A. Case (case_at_scripps.edu)
Date: Tue Jan 25 2005 - 10:40:21 CST

On Tue, Jan 25, 2005, Mayumi Haga wrote:

> I want to ask you about how to make PDB format file of HOPG(graphite)
> substrate. It consists only of carbon, so the amount of C atoms has got
> huge.

Within a given residue, all atom names must be unique. So you might think
if you can somehow divide the graphite into residues, so that you could re-use
atom names.

Alternatively, you will have to be creative in getting unique atom names.
But there may be an upper limit on the size of an individual residue; I'm
not sure about that.

Amber was not designed for this sort of problem, so you will have to be
patient and try various things.

...good luck...dac

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