AMBER Archive (2006)

Subject: Re: AMBER: help creating RNA

From: David A. Case (
Date: Thu Jun 22 2006 - 16:08:45 CDT

On Thu, Jun 22, 2006, wrote:
> I have been fighting with leap in trying to build a simple RNA molecule. I've
> been creating a DNA molecule and then modifying the .pdb file by changing the
> residue names from "A" to "RA" for instance, but leap seems to complain quit a
> bit. Can some one give me a quick protocol as to how to create an RNA molecule?

Just saying: "leap seems to complain quite a bit" is not very helpful. How
about giving some details? Be sure to remove the H2'' atom from you pdb file,
since this atom is not present in RNA. But without more information, one
can really just guess about what might be going on.

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