On 11/15/12 10:41 AM, Steven Neumann wrote:
atomtypes.atp
FE 55.84700 ; heme iron 56
ffnonbonded
FE 9 18.998 0.000 A 0.115816833358244 -0
aminoacids.rtp
[ FE ]
[ atoms ]
FE FE 2.00 0
Hmmmm, confusing...
What force field is that? None of those parameters seem to come from any of the
default force fields in Gromacs. The entry in ffnonbonded is clearly wrong, with
the parameters appearing to belong to fluorine rather than iron, but the line
appears to have been mangled. It looks most like CHARMM, but someone has messed
with ffnonbonded.itp.
Regardless, if you look at the parameters for FE in any of the force fields in
Gromacs, you will see that their nonbonded parameters (C6/C12 or sigma/epsilon)
are generally set to zero. They interact only via ionic interactions because
they were likely only intended for use in cofactors like heme, where other
bonded parameters fix their geometry. Using them as free ions makes little sense.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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