[gmx-users] Fatal Error with AMBER03

Justin Lemkul jalemkul at vt.edu
Fri Dec 14 20:26:01 CET 2012

On 12/14/12 2:22 PM, Eduardo Oliveira wrote:
> Hi,
> I'm trying to use AMBER03 force field with my protein but when i run pdb2gmx i get a fatal error message:
> Fatal error:
> Incomplete ring in HIS415
> The problem is, when I open the structure on pymol i can't see any missing atoms. Does anybody had the same problem?

If all the atoms are indeed present (and checking the text of the coordinate 
file is a much more definitive test), then the only explanation is that they are 
not named in accordance with what the force field requires.  Renaming with a 
text editor is the solution in that case.



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


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