[gmx-users] (no subject)

[Anton Feenstra]

Attila Borics wrote:
> So as I believe I just fitted the backbone of each structure in my trajectory
> to the backbone of reference structure and calculated RMSD for each. Is that right?

That is what it looks like. You can try several things (if you haven't
already). Use g_confrms to compare your original .pdb with the .tpr
file. That should give 0.0 rmsd as well (although, there have been some
quirks with g_confrms). Alternatively, convert the .tpr back to .pdb
(with editconf) and use a program of your choice.

Are you by any chance simulating a multimeric protein? In that case
you may be victim to PBC, with one monomer of the protein on one side
of the box, and another at another side. Check with e.g. rasmol.
In that case, using 'trjconv -nojump', with a reference structure
in which the monomers are still together, should help you out.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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