VMD-L Mailing List

From: kinshuk_at_chem.iitb.ac.in
Date: Sun Oct 14 2007 - 02:21:32 CDT

Hi all,
    I am student of IIT-Bombay. I have been working in the area of de novo
protein designing.Now i have been working on solvation problem there i
have one problem i.e. i have to select water molecule at 5 Angstrong
cutt-off surrounding the peptide in simulation box.
    I have been exploring VMD there i came to know about command (water
within 5 of protein) but when i have given the command it showd the
message invalid command line (water). when i wrote within 5 0f protein
it shows that invalid command line (within). i tried many times it's
all command but it is not working properly.I have been using
VMD-1.8.2.

Please help me.