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

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 3 15:58:25 CEST 2011

Justin A. Lemkul wrote:
> 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.

In addition, you can always renumber any coordinate file using genconf -renumber 
for the purpose of creating index groups.



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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