[gmx-users] impropers and residue number

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 2 15:13:16 CET 2012

Lara Bunte wrote:
> Hello
> I got this error:
> Fatal error:
> Atom ON1 is used in an interaction of type improper in the topology
> database, but an atom of that name was not found in residue
> number 1.
> What do this mean? How to fix it? 
> The Atom ON1 is declared in atomtypes.atp file. 
> In my .rtp file I used [ impropers ] and I use a charmm27 force field.

Impropers are specified in the .rtp file by atom name, not type.  So the error 
indicates that pdb2gmx (?) thinks an atom *named* ON1 should be present, which 
it is not.



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


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