AMBER Archive (2004)

Subject: Re: AMBER: leap problem in AMBER7 (residue insertion)

From: David A. Case (case_at_scripps.edu)
Date: Mon Jul 05 2004 - 12:21:50 CDT

On Mon, Jul 05, 2004, Kuhn, Bernd {PRBD~Basel} wrote:
>
> when leap in AMBER 7 reads the following PDB snippet (residue with an
> insertion code) it will insert an C-terminus and N-terminus into the
> sequence although the residues 105 and 105A are bonded to each other.

Like Scott, I am unable to reproduce the problem; instead, I get the
expected behavior. It is weird that your LEaP doesn't even pick up the ILE
residue name correctly, but then other very strange things are happening as
well (see below).

It looks like your LEaP is treating the "A" in 105a as a chain_id. See
the place where "starting new molecule" is printed out, line 812 in pdbFile.c.
You may have to debug some around here to see how that happened.

> Loading PDB file: ./t.pdb
> (starting new molecule for chain (starting new molecule for chain )

Note that the above message is garbled; maybe some string has overrun memory
or something.

The obvious workaround is to not use insertion codes for the time being.

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu