[gmx-users] Incomplete ring

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 18 15:15:15 CEST 2010

you zou wrote:
> Hi again,
> Thank you, I added missing atoms with emacs, but my question is this ring
> doesn't have to be complete and if I add missing atoms with HIS680's name, I
> change its structure. Is it true?

All structures have to be complete in order for pdb2gmx to process them.  The 
only atoms it can add are hydrogens.  All heavy atoms are required.

If you place the missing atom(s) correctly, according to proper geometry, you 
shouldn't be changing the structure too much, but a simple energy minimization 
after you've generated the topology should relax any poor geometry.


>> Hi Users,
>> I have a .pdb file, in this file when I want to use pdb2gmx command there
>> is this error massage: Fatal error: Incomplete ring in HIS680
>> this aminoacid is not complete in general, I don't know how can I complete
>> this such that I don't add HIS for complete? Please give me a hint.
> add the missing atoms with emacs (or another text editor). Then minimize.
>> Thank you
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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


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