On 7/03/2011 7:33 PM, 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).
Thing is that both the topology and the trajectory are treated equally
at the pdb2gmx step. So how can it be?
You've almost certainly mismatched these files. Only your records can
make sense of what has gone wrong. The source of this folded form has to
be treated in an equivalent fashion (e.g. with another invocation of
pdb2gmx) so that the atom ordering and numbering matches.
Mark
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