AMBER Archive (2003)

Subject: Re: Misaligned Coords from Alanine Scanning

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Fri Feb 07 2003 - 10:00:31 CST

Hi,

> 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 mm_pbsa.in 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

Holger

> 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 http://glycam.ccrc.uga.edu
> 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
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++