[gmx-users] Orders of the residues in gromacs
Du Jiangfeng (BIOCH)
j.du at maastrichtuniversity.nl
Thu Feb 2 18:16:10 CET 2012
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
6200 MD Maastricht
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