[gmx-users] adding iodine

[Magnus Andersson]

> On Mon, 2005-08-01 at 17:17 +0200, Magnus Andersson wrote:
>> Hi all!
>>
>> I'm experiencing problems adding iodine to FF GROMOS96. What I've done
>> is
>> add the following to the force field (in ions.itp):
>
> you have to add it to ffG43a1nb.itp

In the file called ffG43a1bon.itp parameters are already added for the
molecule (which is a retinal):
#define gb_51   0.156   8.0e+06
;
#define gb_52   0.157   8.0e+06
;
#define gb_53   0.152   8.0e+06

The only thing I did was to exchange a carbon
C20 against an iodine I01 in the .pdb file. Then I made the necessary
changes in the .rtp files and ions.itp as already mentioned. I thought I
could keep the definitions already mad for the retinal and pretend that
the iodine is a carbon in terms of bond lenghts, angles etc for the time
being.

This leads to question no 2; where to find correct parameters for an
iodine bonded to a carbon atom?


>>
>> [molecule name]
>> ;molname    nrexcl
>> I-          1
>>
>> [atoms]
>> ; id    at type    res nr    residu name    at name    cg nr  charge
>> mass
>>   1     I-          1         I-            I           1      -1
>> 126.9045
>>
>>
>> And the error message given by pdb2gmx is:
>> 'Atom type I not found in atom type database'
>>
>> What am I missing?
>>
>> /Magnus Andersson
>>
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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