[gmx-users] Fatal error:Atom S in residue TYR 2 not found in rtp entry with 18 atoms

Tsjerk Wassenaar tsjerkw at gmail.com
Tue May 8 06:52:47 CEST 2007

Hi Winter,

> I'm a beginner to GMX,
> when I use the following command:
> "pdb2gmx -f 1G1S.pdb -p gr.top -o gr.gro -missing"

Don't use '-missing'. Since you're a beginner you're not allowed to
(unless you get a permit for it from one of the developers).

> "WARNING: atom CD not found in residue 72 while adding improper

This is the result of using '-missing'.

> Fatal error:
> Atom S in residue TYR 2 not found in rtp entry with 18 atoms
>              while sorting atoms"
> How to solve this fatal error?

Well, as I recall, but I may need to check my biochemistry books here,
there's no S in tyrosine. Is this a modified residue, or is there just
something _else_ wrong with your starting structure? Note that I say
something else, since you clearly also have missing atoms, which you
need to fix. Go work on the starting structure!



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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