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
+++++++++++++++++++++++++++++++++++++++++++++
Received on Fri Feb 07 2003 - 08:00:31 PST
