[gmx-users] grompp Unkown bond_atomtype C2

Justin A. Lemkul jalemkul at vt.edu
Wed May 16 14:08:29 CEST 2012

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 



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


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