[gmx-users] Cannot minimiza - vdwradii.dat ???
s.neumann08 at gmail.com
Thu Nov 15 16:55:49 CET 2012
On Thu, Nov 15, 2012 at 3:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 11/15/12 10:41 AM, Steven Neumann wrote:
>> FE 55.84700 ; heme iron 56
>> FE 9 18.998 0.000 A 0.115816833358244 -0
>> [ 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.
This is charmm27 but modified as you can see. Shall I use:
FE 26 55.84700 2.000 A 0.115816833358 0 0
in original Gromacs charmm it is
FE 26 55.84700 0.000 A 0.115816833358 0.0 ; partial charge def not found
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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