VMD-L Mailing List

From: aiswarya pawar (aiswarya.pawar_at_gmail.com)
Date: Thu Sep 15 2011 - 05:36:25 CDT

Hi VMD users,

I want to calculate the water molecule within a cut off to the protein say
5Angstrom.

i tried doing the cmd-

set sel [atomselect top "water within 5 of protein"] ### but this is for
whole protein, i just need for hydrophobic part of protein, and want to know
which residues present and the distances of these from water. and i need to
output this to a file. is it possible to do a density map of the same.

Thanks,

Aiswarya