AMBER Archive (2006)

Subject: Re: AMBER: change atom in a DNA double strand

From: David A. Case (case_at_scripps.edu)
Date: Thu Jul 06 2006 - 11:57:12 CDT

On Wed, Jul 05, 2006, Carra, Claudio (JSC-SK)[USRA] wrote:

> I'd would like to modify an atom of residue in a DNA double strand.
> The initial geometry from the canonical structure generated by
> nucgen is absolutely fine, but than, I'd like to have a guanine in
> the middle of the double strand replaced the corresponding oxidized one.
>
> it is easy to generate a new library with antechamber for a small molecule,
> but I didn't find any example where a new molecule (not atom) is inserted
> into a macro system.
>
> The error I get and I can't fix is relative to missing parameters
> for the force field, which in general can be fixed by loading frcmod
> file, but not in this case.

Why does it not work "in this case"? What is the error message? Please try
to give details about exactly what you tried, and what the result was.

...thanks...dac

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