AMBER Archive (2009)

Subject: Re: [AMBER] Adding non standard residues

From: David A. Case (
Date: Mon May 11 2009 - 12:30:56 CDT

On Mon, May 11, 2009, Jorgen Simonsen wrote:
> I am trying to modify a water molecule and a cysteine residue from a crystal
> structure - the two residues should be bonded to a nickel ion. I go through
> tutorial 4 "*Simulating a Solvated Protein that Contains Non-Standard
> Residues" *and create the cysteine residue from CYX to CYY and the water
> from WAT to HOC residue names and save the two lib files

> This gives me two problems - first of all the HW-HW is not recognized by

Can't help with the NAMD problem.

> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
> res total affected
> CARG 1
> CYY 1
> HOC 1
> NGLN 1
> WAT 350
> )

I don't think this should cause problems, but you should check to be sure that
the CYY residue is properly bonded to residues before and after it in the

...good luck...dac

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