VMD-L Mailing List

From: Andrés Morales (h.andres.m1986_at_gmail.com)
Date: Wed Apr 11 2012 - 16:43:01 CDT

Hi Jonh,

Thank you so much. I was the problem, now it works so nice.

Andres

2012/4/11 John Stone <johns_at_ks.uiuc.edu>

>
> Hi,
> The source of your problem is that you are calling "return" in your loop,
> therefor the loop terminates after it runs for the first time. The second
> "return" call will never be reached since the first one will end the proc.
> Both versions of the script you sent have that same problem. If you
> want to return results for each lipid, you need to create a list of
> results adding to the end with "lappend" each time through.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Apr 09, 2012 at 12:45:44PM -0500, Andrés Morales wrote:
> > Dear VMD Users:
> > I want to calculate the average angle between the lipid dipole vector
> (P-N
> > dipole vectors in DPPC headgroups ) and the bilayer normal. So I use
> > the following script:
> > proc angle_ave {sel1 sel2} {
> >
> > global M_PI
> > set conv [expr 180.0/$M_PI]
> > set num1 [$sel1 num]
> > set sum 0
> > foreach atom1 [$sel1 get {x y z}] atom2 [$sel2 get {x y z}] {
> > set v [vecsub $atom2 $atom1]
> > set z1 [lindex $v 2]
> > set theta [expr $conv * asin($z1 / [veclength $v] )]
> > set tilt [expr 90 - $theta ]
> > set sum [expr $sum + $tilt]
> > return $tilt
> > }
> > set prom [expr $sum / $num1]
> > return $prom
> > }
> > set sel1 [atomselect top "lipids and resid 1 to 36 and name P "]
> > set sel2 [atomselect top "lipids and resid 1 to 36 and name N "]
> > set average [angle_ave $sel1 $sel2]
> > But it only returns the tilt angle value for the first lipid (resid
> 1).
> > Any suggestions?
> > Thanks a lot
> > Andres
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>