VMD-L Mailing List

From: Mark Zottola (mzottola_at_gmail.com)
Date: Thu May 17 2007 - 16:44:10 CDT

I am new to VMD and would like to be able to do some things which do not
(apparently) exist in the manual.

1) I would like to be able to take and generate pdb files from a select
number of frames from and MD simulation.

2) I would like to be able to monitor the number of water molecules near an
active site residue over the course of a simulation as well as calculate
distances of these waters from a particular atom in the active site..

3) I would like to monitor the distance between two atoms in 2 different
residues over the course of a simulation.

Are these best done by writing a Tcl script? Are there built in functions
to do this?

Thanks for any help you can send my way!

Mark