VMD-L Mailing List

From: _at_huji.ac.il
Date: Thu Dec 21 2006 - 05:09:59 CST

Dear Sir,

My name is Regina and I'm a PhD student. I hope you will be so kind and be able to help me with my problem. I need to calculate the number of water/glycerol molecules in a
predefined radius around the peptide. I have a trajectory after
simulation. During the simulation my peptide is drifting to the PBC
borders. When I used the selection "water and within * of
resid VMD showed the water molecules within the distance, but only
those inside the box. When I turn on peridoic cell in the direction
peptide drifting, VMD still wouldn't show those water molecules. Neither did they
appear on the other side of the water box. As I understand
this is known issue of vmd - it is not 'pbc enabled'.

I have tried to use tcl script from VMD script library (color_coord.tcl)in oder to build replicas of
central box and after that to calculate the the number of molecules
but the script didn't work. Can you please be so kind and help me with
this problem. The modified script is attached. You can also see the output I'm geting when trying to run it.

Best regards
Regina

shifting by 0.0 0.0 0.0
building segment R0
setting patch for first residue to NONE
setting patch for last residue to NONE
Info: generating structure...
Info: segment complete.

no residue 5 of segment R0
ERROR: failed on coord
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.