[gmx-users] grompp Unkown bond_atomtype C2

[Justin A. Lemkul]

On 5/16/12 8:05 AM, Lara Bunte wrote:
> Hi
>
>
> in my .rtp file I wrote in the [ atoms ] block
>
> C2   CN1A    0.7481   1
>
>
> but in the atomtypes.atp file I wrote
>
> CN1A    12.01100
>
>
> So I declared it. So what do you mean with "such an atom type doesn't exist"?
>

Neither of those actions constitutes what you need.  Your atom name is C2, while 
its type is CN1A.  Apparently somewhere in the bonded parameters you've assigned 
C2 as a type, which is wrong.  You need to be using CN1A if adding a new bonded 
parameter.  The CN1A atom type already exists in the force field so you don't 
need to do anything special.

Note for the future that in order to add a new atom type (if necessary), it 
needs to have its parameters listed in ffbonded.itp.  Mentioning it in the .rtp 
and .atp files does not do much for you; it simply makes that atom type 
accessible in the topology, but if it doesn't have parameters assigned, it is 
useless.

-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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