VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Jul 09 2011 - 18:33:24 CDT

On Sat, Jul 9, 2011 at 6:48 PM, Simulation Biology
<supercomputer.simulation_at_gmail.com> wrote:

> Hi all,
>
> I am trying to use the PBCwrap tools and I belive I am doing something
> wrong. I want to wrap water molecules that have a z-axis compoent smaller
> than a specifc number; and I don't know how to do it?  What I did is just
> try to move the water from one unit cell to another and keep the protein in
> the original unit cell by using the following command
>
> pbc set {154.1451 147.6427 286.8863} -all
> pbc wrap -sel "water"  -orthorhombic -shiftcenterrel {1 0 0 }
>
> However I  see that the water molecule's bonds got stretched out. Then I
> read again the manual and I cannot figure out how to use the compound
> command.
>
> -compound res[id[ue]]|seg[id]|chain|fragment

the square brackets ([]) denote optional parts of a string
and the pipe character (|) alternatives. this is a _very_
common shortcut notation. thus this line expands into
the following alternatives

-compound res
-compound resid
-compound residue
-compound seg
-compound segid
-compound chain
-compound fragment

> can anyone help me and explain with a example hot to use it? I mean how to
> let know the tools that you are using the residue WAT for water.

the default of pbc tools is to wrap based on individual atoms.
if you want to keep (water) molecules complete, you can use

-compound fragment

or (since each water molecule is a separate residue)

-compound res
or
-compound resid
or
-compound residue

axel.
>
> Thanks for your help and sorry if this is a stupid question.
>
> --
>
> Cheers
>
> Molybdenum

p.s.: i miss the old times, where people said who
they were and would not use pseudonyms and/or
randomly named e-mails addresses... 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.