VMD-L Mailing List
From: Olaf Lenz (lenzo_at_mpip-mainz.mpg.de)
Date: Sun Jul 12 2009 - 03:00:58 CDT
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Hi!
Angelo Rossi wrote:
> I am not sure what the error about rlwrap means. Perhaps, it is related
> to my problem below.
rlwrap has nothing to do with pbctools.
> The protein+bilayer now seems to be centered inside the cube, but the
> surrounding water is really in a tangle.
> There are bonds to water from one side of the cube to the other.
In general, it might help to have a look at the documentation:
http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
> With pbctools v2.4, the above commands were sufficient, and the
> structure and water were wrapped fine.
Are you sure that you are talking about pbctools 2.4, or pbctools 2.1,
that was distributed with VMD 1.8.6?
> But now, pbctools v2.5 gives different behavior.
Indeed - with version 2.2 I changed the default for the "-compound"
option to "nocompound", which means that by default it will wrap all
atoms, regardless of whether they belong to a compound (e.g. a water
molecule) or not. To get back the "old" behaviour, use
pbc wrap -compound res
which will wrap atoms, but keeps residues together, assuming that in
your setup all water molecules are single residues.
Best regards
Olaf
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