Thanks! I did overlook that.
Quoting David van der Spoel <[email protected]>:
On 2010-08-24 22.53, [email protected] wrote:
Hello,
I converted a .tpr file for Bromine ion and Potassium ion using -mead
option and editconf. It gives out the Van der Waals radius of the atom,
but I don't understand why i got ~2.46A for Potassium and ~2.31A for
Bromide. Isn't the bromide ion bigger than Potassium? And I used genion
to add both the atoms.
This is a force field quirk. From the oplsaa.ff/ffnonbonded.itp
[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name bond_type mass charge ptype sigma epsilon
opls_402 Br- 35 79.90400 -1.000 A 4.62376e-01 3.76560e-01
opls_408 K+ 19 39.09830 1.000 A 4.93463e-01 1.37235e-03
You see that K+ has larger sigma than Br-.
Thanks.
-Nisha P
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
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