AMBER Archive (2008)

Subject: Re: AMBER: Leap atoms CL and OXT do not have a type

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sat Sep 27 2008 - 09:12:40 CDT

On Sat, Sep 27, 2008, Francesco Pietra wrote:

> I have a problematic pdb file for leap (or for me!). It is for a
> multimer created with Modeller and contains chloride ions ligands.
>
> Created a new atom named: OXT within residue: .R<LYS 420>

Do you have a TER card between residue 420 and 421? This is needed so
that Amber knows that Lys 240 is at the end of the chain, and hence
should have an OXT atom.

> Creating new UNIT for residue: CL sequence: 421

The Amber residue name for a chloride ion is "Cl-", and the
corresponding atom name is "Cl-" as well. You will probably need to
adjust your pdb input file.

[Do people know if "CL" is really a pdb/rcsb supported standard? If so,
we should probably either update ions08.lib, or add appropriate
translation lines in the standard leaprc files.]

...dac

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