[gmx-users] Orders of the residues in gromacs

Jianguo Li ljggmx at yahoo.com.sg
Fri Feb 3 03:04:28 CET 2012

Another possible reason is due to vmd, which numbers the residue from 0. Residue 143 in gromacs corresponds to residue 142 in vmd.


 From: Du Jiangfeng (BIOCH) <j.du at maastrichtuniversity.nl>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org> 
Sent: Friday, 3 February 2012, 1:16
Subject: [gmx-users] Orders of the residues in gromacs

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? 

Thank you in advance,


    Jiangfeng Du, PhD Student
    Cardiovascular Research Institute Maastricht
    Department of Biochemistry
    P.O. Box 616
    Mobile: +31-681741859
    FAX: +31-43-3884159
    6200 MD Maastricht
    The Netherlands--
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