BIN ZHANG wrote:
Hi, there:
I found that in gromacs version 4.5.1, the residue ids are not ordered
consecutively as before in the .gro file. For example, if I have two
chains in the protein, then the residue ids will be ordered with respect
to each individual chain, rather than reordered to be a complete system.
I also attached one segment in the gro file for illustration.
Is this supposed to be a new feature? It's actually quite inconvenient
when trying to make selection in VMD.
The default behavior is now to not renumber the residues in the original
coordinate file passed to pdb2gmx. I suspect that there were missing residues
at the N-terminus of your second chain, at least. To disable the feature, use
pdb2gmx -renum.
-Justin
Thanks,
Bin
==========================
816VAL HG1313296 3.455 7.611 11.465 0.7230 -0.9675 -4.0812
816VAL CG213297 3.630 7.461 11.621 -0.5958 0.7701 0.1938
816VAL HG2113298 3.680 7.555 11.591 0.2600 0.8421 1.7585
816VAL HG2213299 3.571 7.503 11.705 2.5960 0.5799 2.7250
816VAL HG2313300 3.714 7.394 11.646 -0.5850 1.1199 1.1233
816VAL C13301 3.390 7.261 11.629 -0.6898 0.0472 -0.1581
816VAL OT113302 3.270 7.268 11.592 -0.7354 -0.1123 -0.0378
816VAL OT213303 3.418 7.233 11.749 0.0205 0.1649 -0.2904
8ALA N13304 4.101 8.322 6.962 0.4051 -0.3543 -0.0582
8ALA H113305 4.012 8.374 6.969 1.1832 1.0474 -0.2561
8ALA H213306 4.179 8.374 7.007 -0.8226 0.0271 1.7227
8ALA H313307 4.089 8.236 7.020 -2.0801 -1.0654 -1.4588
8ALA CA13308 4.132 8.290 6.820 0.4700 0.4977 -0.2390
8ALA HA13309 4.051 8.228 6.785 -1.3315 1.9366 1.1423
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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