[gmx-users] (no subject)
feenstra at chem.vu.nl
Mon Aug 18 10:05:04 CEST 2003
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.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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