AMBER Archive (2006)

Subject: Re: AMBER: leap can't assign CALA

From: David A. Case (
Date: Fri Sep 22 2006 - 19:53:29 CDT

On Fri, Sep 22, 2006, Myunggi Yi wrote:

> Created a new atom named: OXT within residue: .R<ALA 392>
> WARNING: There is a bond of 25.854368 angstroms between:
> ------- .R<ALA 392>.A<C 9> and .R<FE2 393>.A<FE2 1>

This example exposes a long-standing buglet in LEaP: The "TER " card
separating molecules must have a space following the letters TER. This is
probably true for official PDB files, but is just asking for trouble, since
the missing white space is not visible in text editors, etc.

For now, just edit your pdb file, and make sure that each TER card has a space
after the "R". I'll post a patch that removes this restriction.

Thanks for the report. (I hope this will solve the problem you see; if not,
please let us know.)


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