hello:
I am preparing prmtop/inpcrd for a protein in a tip3 water box with ca
0.6M NaCl. Ambertools12.
I used concanavalin-derived parameters for the Ca(II) ions present and
frcmod.ionsjc_tip3 for the monovalent and water.
The protein was first solvated (TIP3PBOX 12 0.5), then neutralized
(Na+ 0), and finally
addions x Na+ 200
addions x Cl- 200
Numerous Cl- ions (and only them) are seen outside the box.
The max distance of the Cl- ions from the box sides is about 10A (the
box vdw is 85 85 80)
I am aware of old and recent similar issues on the list, and about the
limit of the parameterization of Ca(II). I am wondering whether there
are new fixes or suggestions about (and whether the ensemble, as such,
could be run on NAMD; unfortunately, I have GPU access with NAMD only
and, to spare on the electricity bill, the large CPU cluster is no
more in use).
Thanks for advice.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 01 2012 - 02:00:03 PDT
