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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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