[gmx-users] Cannot minimiza - vdwradii.dat ???

Justin Lemkul jalemkul at vt.edu
Thu Nov 15 16:47:33 CET 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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