VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Feb 12 2009 - 07:40:14 CST

You would need to do some scripting for this, something like (not tested)

foreach molid [molinfo list] {
    set sel1 [atomselect $molid "resid 615 and name OP1"]
    set sel2 [atomselect $molid "resid 900 and name OG"]
    set ind1 [join [$sel1 get index]]
    set ind2 [join [$sel2 get index]]
    $sel1 delete
    $sel2 delete

    puts [measure bond [list $molid $ind1] [list $molid $ind2]]
}

Note that if the indices of the two atoms you care about are the same in
all molecules, you don't need to use atoms selections to define ind1 and
ind2. If all of your molecules have the *same* number of atoms, then you
ought to load them all into one molecule as a trajectory instead, which
makes this much easier.

Best,
Peter

bo baker wrote:
> Hi, VMD:
>
> I have a set of pdb files and would like to plot the atomic distances
> from all of them. I ckecked "Lable" and "VolMap" tools. Both gives the
> distance from individue files but not of the all files.
>
> Can any one suggest if VMD could perform this task? For example, I
> would like to know the distance between 615 O1P and 900 OG through the
> entire pdb filed loaded.
>
> Thank you for your advice
>
> Bo
>