Sergio Manzetti wrote:
Hello, I am doing a refolding experiment, but I re-experience the same
error. First of all, I use pdb2gmx for an input PDB structure, choose
OPLS/AA force field and vacuum settings (no waters).
Then I amke a box, and start simulations.
What I want to do is to compare the starting unfolded structure of the
simulation and its changes during the sim (all represented as a
traj.xtc) to a native folded conformation of the structure. Assuming it
to be possible, I thought of using g_rms;
g_rms -f native-folded.gro -s topol.tpr
Then I get the same error message:
WARNING: topology has 497 atoms, whereas trajectory has 491
-------------------------------------------------------
Program g_rms, VERSION 4.5.1
Source code file: mshift.c, line: 102
Fatal error:
Molecule in topology has atom numbers below and above natoms (491).
Either (1) you're not saving the right atoms during the simulation (xtc-grps) or
(2) you're choosing to analyze a non-existent group with g_rms, or a combination
of both. For better diagnostics, provide your .mdp file, a description of your
system, and your g_rms command line.
Thing is that both the topology and the trajectory are treated equally
at the pdb2gmx step. So how can it be?
pdb2gmx only deals with coordinate files in order to produce the topology. Your
trajectory is irrelevant here, but if you've somehow tried to manipulate your
trajectory or its contents with pdb2gmx, then you can be sure that this is
what's causing your error.
-Justin
Sergio
--
========================================
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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