VMD-L Mailing List

From: Caio S. Souza (caiobiounb_at_gmail.com)
Date: Wed Dec 19 2012 - 07:30:38 CST

Hello

In your script you must update your selection and write a .pdb file
for each frame. Like this:

set sel [atomselect 0 "water and within 4 of resid 289"]
for {set i 0} {$i < [molinfo 0 get numframes]} {incr i} {
    $sel frame $i
    $sel update
    $sel writepdb your-name.$i.pdb
}

Cheers

2012/12/19 Albert <mailmd2011_at_gmail.com>:
> hello:
>
> I found a problem of the selection in VMD, I would like to export the
> solvent molecule within 4 of resid 289 for each frame and I use the
> following syntax for this purpose:
>
> water and within 4 of resid 289
>
> When I open this exported file in pymol, I found that there are water
> molecules within 4 of resid 289 in the first frame instead of each own
> frame, it is some kind of the movement of the water molecule in the first
> frame within 4 of resid 289......I am just wondering, how can I export the
> water molecules for each frame within 4 of resid 289?
>
> THX
> Albert 

-- 
Caio S. Souza
Laboratório de Biofísica Teórica e Computacional
Universidade de Brasília