Another possible reason is due to vmd, which numbers the residue from 0.
Residue 143 in gromacs corresponds to residue 142 in vmd.
Cheers,
Jianguo
________________________________
From: Du Jiangfeng (BIOCH) <j...@maastrichtuniversity.nl>
To: "gmx-users@gromacs.org" <gmx-users@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.
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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