AMBER Archive (2004)

Subject: Re: AMBER: How to make leap recognise inosine?

From: Rhonda Torres (torres_at_scripps.edu)
Date: Tue Mar 23 2004 - 11:54:49 CST

On Tue, 23 Mar 2004 arvind_at_mbu.iisc.ernet.in wrote:

> Hi all,
> i'm new to amber and my pdb file contains inosine residues. On using
> 'loadpdb' command, leap complains the following:
>
>
> Loading PDB file: ./inosine.pdb
> Unknown residue: I number: 3 type: Nonterminal
> Unknown residue: I number: 15 type: Nonterminal
> Creating new UNIT for residue: I sequence: 4

> Can somebody please suggest how do i make leap recognise inosine? Would i
> also require a new parameter set for inosine?
>
> Regards,
> Arvind.
>

You would need to create the residue inosine (i.e. inosine.in). Please
see the plastocyanin tutorial to guide you in creating this residue as
well as adding any necessary parameters.

Rhonda

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