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

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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