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

[Steven Neumann]

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:
>>
>> 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
>

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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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