Re: Misaligned Coords from Alanine Scanning

From: Holger Gohlke <>
Date: Fri 07 Feb 2003 08:00:31 -0800


> We are trying to replace a lysine with an alanine. When we run AS, the
> analine coordinates in the resulting snapshots are incorrect. We are using
> the parmtop file for the lysine-containing (wild type) protein, which
> correctly generates the snapshots for the wildtype, but as I say with AS it
> appears to be aligning the alanine incorrectly.

I don't quite understand - for _generating_ Ala-substituted coordinates
from the coordinate files, no parmtop file is necessary. For
calculations thereafter, a modified parmtop file (of the mutant protein)
needs to be used.

> I'm using the atom numbers from the wildtype protein as the pointers for the
> CG, CB and C atoms in the lysine.

I can't really say from this what might be going wrong. Perhaps you can
send me your file along with (part of) the crd file and the
wild type and mutant parmtop files? By the way - which amber version do
you use?

Best regards


> Any help would be much appreciated.

> Robert J. Woods, Ph.D.

> Associate Professor of Biochemistry Voice: (706) 542-4454
> and Molecular Biology FAX: (706) 542-4412

> University of Georgia
> Complex Carbohydrate Research Center
> 220 Riverbend Road "One small step for Man,
> Athens, GA 30602 one giant leap for Man-9"

Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
Received on Fri Feb 07 2003 - 08:00:31 PST
Custom Search