VMD-L Mailing List

From: VISWANADHA SRIDHARA (vsrid001_at_odu.edu)
Date: Thu Sep 08 2005 - 10:29:54 CDT

Hi VMD users,

I am trying to get the resid's of the molecules in a trajectory.

The script I wrote I have seen in VMD tutorial is

set number_frames [molinfo top get numframes]
set selection [atomselect top "exwithin 3 of protein"]
for {set i 0} {$i < $number_frames} {incr i} {
$selection frame $i
$selection update
$selection writepdb water_$i.pdb
}

Now I want to find the residue ID's of the water molecules in water_$i.pdb
files.
Is there any straight coding which can be incorporated in the script to
directly get residue ID's in a notepad/wordpad file.
I can use gromacs or other tool to convert each water_$i.pdb file to
water_$i.ndx file, but can I use "$selection get index" and then store that
in a file(ofcourse not pdb).

Thanks in advance and Best Regards,
Viswam.