VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Feb 08 2011 - 16:25:00 CST

On Tue, Feb 8, 2011 at 4:15 PM, <larac_at_berkeley.edu> wrote:
> Hi Dr. Kohlmeyer,
>
> I am afraid I'm still a bit confused--all of these variants fail and I
> can't figure out the correct syntax from the manual.
>
> vmd > volmap ils $sel -minmax {{-68 -77 -80} {68 77 80}} -dx output.dx
>
> vmd > volmap ils $sel -minmax {{-68 -77 -80} {68 77 80}} -allframes
> -combine pmf -dx output.dx -dihomo -probe1 -0.12 1.70 -bond 1.12 -conf 50
> -cutoff 12 -subres 2
>
> vmd > volmap ils $sel -minmax {{-68 -77 -80} {68 77 80}} -allframes
> -combine pmf -dx output.dx -dihomo -probe1 -0.12 1.70 -bond 1.12 -conf 50
> -cutoff 12 -subres 2
>
> The error is always:
>
> expected integer but got "atomselect6"volmap: molecule specified for ouput
> is invalid. (-mol)

i have to repeat myself, the volmap ils command obviously takes a different
sequence of arguments. the first argument is a molecule id and not a selection.
here is volmap commandline has it is constructed by the ILS plugin:

volmap ils $molid $minmax -cutoff $cutoff -res $res -subres $subres
-orient $orient \
 -alignsel $asel -maxenergy $maxen -T $T -o $dxfile"

as you can see this is different from what you are using
and consistent with the error message that you are getting.

axel.

> Thanks for responding; I really appreciate it.
> Lara
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.