VMD-L Mailing List

From: Simulation Biology (supercomputer.simulation_at_gmail.com)
Date: Sat Jul 09 2011 - 17:48:29 CDT

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

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.

Thanks for your help and sorry if this is a stupid question. 

--
Cheers
Molybdenum