[gmx-users] parameterization of new metal ion

[Justin A. Lemkul]

On 5/17/12 5:12 AM, priya thiyagarajan wrote:
> hello sir,
>
> thanks for your kind reply..
>
> while setting new parameters for metal ion NI2+
>
> i edited my ions.itp by including the following lines..
>
> [ moleculetype ]
> ; molname   nrexcl
> NI          1
>
> [ atoms ]
> ; id    at type res nr  residu name at name  cg nr  charge   mass
> 1       NI2+    1       NI          NI       1      2        57.9339
>
>
> also edited .rtp file by including the following lines
>
> [ NI ]
>   [ atoms ]
>     NI  NI2+     2.00000     0
>   [ bonds ]
>   [ angles ]
> ;  ai    aj    ak   gromos type
>   [ impropers ]
> ;  ai    aj    ak    al   gromos type
>   [ dihedrals ]
> ;  ai    aj    ak    al   gromos type
>
> but still i am getting the error
>
>
> Fatal error:
> Atomtype NI2+ not found
>
>
> can you tell me how to solve this error..
>

Parameters for all atom types must be listed in ffnonbonded.itp, and 
atomtypes.atp if you're having pdb2gmx build the topology (which is also where 
the .rtp entry comes into play).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
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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