[gmx-users] bug in editconf for making a box ? combined two residues into one

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 3 15:55:21 CEST 2011

maria goranovic wrote:
> Thanks for the replies. I guess it is a very small bug. However, here is 
> another:
> I have a 2-protein complex in water. The first protein residues numbers 
> are from residues 4 to 14, and the other from 5 to 9. In the INPUT .gro 
> file to grompp, I have a continuous numbering of residues from 4 to 19 
> (4 to 14+5). However, after an energy minimization, gromacs writes out a 
> .gro file which preserves the original numbering (4 to 14 and 5 to 9) 
> instead of a numbering from 4 to 19. Why does it do that? I can see the 
> problem with such a numbering because I can never unambiguously select 
> "residue number 6" if I want to make an index file. How does one go 
> about fixing this? 
> I made the original input .gro file by using : editconf -f in.gro -o 
> out.gro -resnr 4
> In the topology file, I read in protein_A.itp and protein_B.itp which 
> start from the original pdb residue number (4 and 5 respectively for the 
> two chains)

This is expected behavior and arises from pdb2gmx.  The default is pdb2gmx 
-norenum, preserving the original residue numbering.  The feature was 
implemented to make selections less ambiguous in the case of missing residues 
(i.e. termini).  You can get continuous numbering, if you wish, by recreating 
the topology with pdb2gmx -renum.



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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