From: Olaf Lenz (
Date: Sun Jul 12 2009 - 03:00:58 CDT


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:

> 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