[gmx-users] trjconv -pbc: how to keep all parts of the system "clustered" together in PDB?
Mark.Abraham at anu.edu.au
Wed Dec 23 01:29:26 CET 2009
Visvaldas K. wrote:
> Dear GROMACS users and gurus,
> I am sorry if it's a stupid question...I'm fairly new GROMACS, and something is been driving me crazy. I have a protein, two metal ions, and inhibitor in my system. Somehow in some of the frames I can't keep all those pieces "clustered" compactly for some postprocessing, using trjconv for conversion of trr/xtc into PDB format:
> "-pbc mol" option of trjconv: metal ions are far from the rest of the protein.
> -pbc nojump or -pbc whole: inhibitor far from the protein, metals are fine.
> -pbc atom or -pbc res: couple of residues are disattached from the protein; metals and inhibitor are fine.
> -pbc cluster: doesn't work (irrelevant?)
-pbc cluster should work with a suitable index group of
protein+metal+inhibitor - that's what it is for.
Once that's done, you may want to re-run trjconv to apply other effects.
Two-pass processing is often necessary.
> Also -center and -boxcenter don't seem to help...
> Can anybody suggest some tricks? I used octahedral box for my runs.
"don't seem to help" also doesn't help. We can't guess what it was about
your inputs and outputs that was contrary to your hopes :-)
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