AMBER Archive (2008)

Subject: RE: AMBER: PF6 parameters

From: caoch (
Date: Thu Mar 27 2008 - 23:28:03 CDT

Dear Aneesh:


 Below is only my personal suggestion.


  Although I don't know what your research aim is, if you want to do a PF6
system simulation with Amber, you can choose the OPLS forcefield (Since the
OPLS forcefiled is very similar to AMBER forcefield).

Notice before running Sander, you should redefine the definitions of
geometric combining of Lennard-Jones radius by changing "radius(i,j) = 0.5 *
(radius(i) + radius(j)) " to "radius(i,j) =sqrt(radius(i) *radius(j)) in the
source code.


 Some other universal force field such as Compass and Polarizabe force field
such as Lucretius also support PF6. But all of them are not compatible due
to the large different definitions of the forcefield potential.



JST-CREST Researcher
Fundamental Technology Laboratory
Research and Development Division
Mitsubishi Chemical Group Science and Technology Research Center, INC.
1000 Kamoshida-cho, Aoba-ku, Yokohama 227-8502, Japan
TEL +81-45-963-3264


From: [] On Behalf Of
aneesh cna
Sent: Thursday, March 27, 2008 1:44 PM
Subject: AMBER: PF6 parameters


Respected amber users,
                     Anyone have force field parameters( stretching and
angle) for PF6 anion?.

Thanks in advance

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