Re: [AMBER-Developers] Chirality routines in tleap; do they do the correct thing with coordination numbers >4

From: B. Lachele Foley <>
Date: Thu, 17 Nov 2011 16:35:52 +0000

Ah... chirality. This is an old issue in tleap, and it doesn't only affect higher coordination numbers. I'm trying to remember if/when/how any of us said anything about it. I fear that by the time we found workarounds, the combined effects of exhaustion, frustration and anticipation of another hour or two to generate a coherent bug report resulted in forgetting entirely to mention it to anyone else.

We always have to double-check our structures to be sure an alpha sugar has not suddenly been made beta. This occurs in some situations when using the sequence command. I think sleap did this too, but can't be sure. I can provide an example, if desired. The workaround... oh... I think involved very careful fragmenting and ordering when building the structures and in setting heads and tails much more often than should be necessary.

Another puzzling behavior is that the copy command will invert chirality (anomeric center only, as I recall) in certain cases. The fix to this was simple -- copy twice.

In a possibly related bug... we have found that in some situations, a subsequent impose command will be applied to all previous impose's.

Sorry I don't know the code involved in that, and I don't think any of the rest around here do, but these semi-related behaviors might help find the trouble.

:-) Lachele

Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA

From: Mark Williamson []
Sent: Thursday, November 17, 2011 11:13 AM
To: AMBER Developers Mailing List
Subject: [AMBER-Developers] Chirality routines in tleap; do they do the correct thing with coordination numbers >4

Dear All,

I'm currently hitting an issue within tleap when loading a PDB file
corresponding to a predefined residue. Specifically, it is being
triggered when tleap adds a missing heaving atom which is absent the
PDB. The reside is a heme residue in the compound I state and the PDB is
missing the ferryl oxygen (O1).

I've entered this in AMBER's bugzilla with lots more information and a
test case:

I'd be really grateful if someone more familiar with this code could
perhaps suggest some new ideas for me to try with respect to this.



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Received on Thu Nov 17 2011 - 09:00:04 PST
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