[gmx-users] Orders of the residues in gromacs

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 2 18:43:17 CET 2012

Du Jiangfeng (BIOCH) wrote:
> Dear Friends,
> I want to measure some data of a special residue, for instance TRP143, from my MD result. But i encountered a problem. 
> The residue number 143 is ordered in .gro file, while it seems the residue orders is random in gromacs. It points to another residue when I specify residue number 143 in VMD or when I am using make_ndx program ( --> r 143; q). Apparently, gromacs numbering system is not based on the orders in the .gro structure file. 
> Does anybody know how to link the gromacs order to the structure file's order correctly? 

Depending on the Gromacs version you're using, residue numbering is treated 
differently.  In pdb2gmx, you can choose to renumber the residues from 1 or not. 
  The default is to not renumber the file.  You should check to see what you did 
with respect to this option and whether or not your coordinate file is numbered 
from 1.  If it is not, then what you think is residue 143 may not be interpreted 
that way by all external programs, depending on whether or not they respect the 
numbering of the .gro file.



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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