[gmx-users] Both atom and residue type four letters . . .

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 6 20:49:52 CEST 2009

Marc Charendoff wrote:

> Fatal error:
> Atom ZN2+ in residue ZN2+ 1 not found in rtp entry with 1 atoms
> while sorting atoms

This means your .pdb file format is fine.  Unfortunately (and I missed this the 
first time, too), the only thing wrong is the atom name.  In ffG43a1.rtp:

[ ZN2+ ]
  [ atoms ]
    ZN  ZN2+     2.00000     0

ZN = atom name
ZN2+ = atom type

So you don't actually deal with a 4-character atom name.  Make ZN the name of 
the atom, keep ZN2+ the name of the residue, and maintain proper formatting. 
Everything should work if all of those conditions are satisfied.



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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