Amber protein-ion problem

From: <>
Date: Tue 11 Jun 2002 13:41:29 +0200


I am studying a protein with total +3 charge after protonation. I have added
three Cl- ions using xleap ("addions unit Cl- 0"), but when I start an
sander minimisation the three ions end up close together (less than an
Angstrom from each other) close to the border of the solvent. I have
solvated the protein with a cap of water molecules with a radius of 35
Angstrom. Why does it happen like this? It does not seem correct to me. Do
you know what is wrong and what I can do to make it work?
I use Amber version 6.

Best regards,

Emma Sigfridsson

PS. There is another little thing with xleap (no real problem). If I start
by solvating the protein and then add ions just two are added (instead of
three if I do it in the opposite order). When I check the unit using "edit
unit" and "check unit" it shows that there is a plus charge. Confusing, but
not a real problem... I just wanted to let you know.

Emma Sigfridsson
Computational Chemistry
Medicinal Chemistry
R&D Mölndal
431 83 Mölndal
Phone: +46 31 706 47 64
Received on Tue Jun 11 2002 - 04:41:29 PDT
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