From: Angelo Rossi (
Date: Sun Jul 12 2009 - 08:02:21 CDT

Dear Olaf Lenz:

Thanks so much. It worked!!!

 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.

This is correct. It's really related to the startup of vmd. rlwrap is a
readline wrapper which is related to parsing.**

> 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:

I really did 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?
You are probably correct about this. I was using VMD 1.8.6 but reading the
pbctools v2.4 documentation. I stopped the project for a while, reinstalled
VMD v1.8.7b5 and then discovered the changed in behavior.

> 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.

Excellent!! Tthis worked!!!

May I suggest that perhaps more examples be added to the documentation.

 The way in which **I proceed when using most software is to read over the
documentation quickly, look at the examples, and try to link the examples
back to the documentation and move forward on my particular problem. For
example, my problem, that of a solvated protein or (other solvated entity),
is the most typical situation one finds in MD. An example of this along
with what you said above would be really helpful in the documentation.

Thanks again so much for your help and quick response.

Warm regards,