From: L. Michel Espinoza-Fonseca (
Date: Tue Mar 07 2006 - 07:11:21 CST

Hi Axel,

I tried to do what you suggested me, but it didn't work. Maybe I did
it wrong. First, I used the script called "moveframes.tcl" as:

moveframes top water

then I continued to the next steps to set PBC (my file is in DCD
format). Then I tried to perform the analysis I wanted to, but I got
the same results.

Do you have any suggestions?



2006/3/6, Axel Kohlmeyer <>:
> On Mon, 6 Mar 2006, L. Michel Espinoza-Fonseca wrote:
> dear michel,
> if you have enough water around your peptide, the following may work:
> load the trajectory, then use a hacked version of the fitframes
> script, that does only move the selection, and apply pbc.
> depending on your trajectory format (some do store the box information,
> some not), you have to set the box dimensions as well (see set_unitcell)
> and then apply pbc based on the thusly stored info (i have used a hacked
> version of pbcwrap for that, attached). so that in the end you you
> something like:
> source set_unitcell.tcl
> source pbcwrap.tcl
> mol new waitfor all
> set_unitcell 11.0 11.0 11.0
> pbcwrap
> animate goto 0
> and then do your analysis.
> good luck,
> axel.
> MEF> Dear all,
> MEF>
> MEF> I've been trying to analyze the contacts between water and a given
> MEF> peptide from my trajectories. I used a nice script provided by one of
> MEF> the VMD users. Everything went well, except from the fact that VMD is
> MEF> not able to count the water molecules around my peptide from the image
> MEF> of my periodic box. I've read some issues related to the pbc and VMD
> MEF> (computation of hbonds, for instance), and according to what I read,
> MEF> there is not such handling of pbc in VMD. Do you have any suggestions?
> MEF> I tried to use some artifacts such as drawing images of the water box,
> MEF> but it didn't work.
> MEF>
> MEF> Thanks!
> MEF>
> MEF> Michel
> MEF>
> --
> =======================================================================
> Axel Kohlmeyer
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.