AMBER Archive (2005)

Subject: AMBER: wierd behavior of addions

From: jz7_at_duke.edu
Date: Tue Mar 22 2005 - 13:22:54 CST

Dear all,

I was following the amber tutorial to set up a MD simulation. The
structure is the pdb file I got from protein data bank. When I tried to
add counter ions to the system, all the Na+ atoms are on one side of the
protein and the ions are actually in one line. I did several times and all
get the same wierd behavior. Is this normal? Could anyone please explain
why this is happening?

Thanks a lot!

The output of xleap is the following:

> addions pro1 Na+ 0
6 Na+ ions required to neutralize.
Adding 6 counter ions to "pro1" using 1A grid
Grid extends from solute vdw + 1.87 to 7.87
Resolution: 1.00 Angstrom.
grid build: 0 sec
 (no solvent present)
Calculating grid charges
charges: 36 sec
Placed Na+ in pro1 at (85.41, 13.04, 11.37).
Placed Na+ in pro1 at (87.41, -14.96, 18.37).
Placed Na+ in pro1 at (66.41, 29.04, 21.37).
Placed Na+ in pro1 at (72.41, -15.96, 29.37).
Placed Na+ in pro1 at (86.41, 30.04, 19.37).
Placed Na+ in pro1 at (94.41, -2.96, 29.37).

Done adding ions.

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