VMD-L Mailing List

From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Jul 06 2011 - 09:53:32 CDT

Dear VMD users,

 Thank you very much for your time and help. I will test the script and let
you know the results. Once again thanks a ton for your help.
S

On Wed, Jul 6, 2011 at 5:56 AM, sajad falsafi <sajad.falsafi_at_yahoo.com>wrote:

> Hi
>
> I acknowledge from Dr. Axel Kohlmeyer for his helpful suggestions.
> We Write a Script to calculate the distance between atoms in big DCD files.
>
> proc distance { frame } {
> global all sel1 sel2 coord1 coord2 outfile
> set coord1 [lindex [$sel1 get {x y z}] 0]
> set coord2 [lindex [$sel2 get {x y z}] 0]
> puts $outfile "$frame: [vecdist $coord1 $coord2]"
> }
> set outfile [open distance.dat w];
> set mol [mol new protein.psf waitfor all]
> mol addfile protein.pdb type pdb waitfor all
> set sel1 [atomselect $mol "protein and resid 1 and alpha"]
> set sel2 [atomselect $mol "protein and resid 2 and alpha"]
> bigdcd distance eq-0.dcd eq-1.dcd
> bigdcd_wait
> close $outfile
>
>
> Hope this helps you
> Sajad & Zahra
>
> ------------------------------
> *From:* Axel Kohlmeyer <akohlmey_at_gmail.com>
> *To:* snoze pa <snoze.pa_at_gmail.com>
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Sent:* Wed, July 6, 2011 5:40:04 AM
> *Subject:* Re: vmd-l: Distance between atoms in frame
>
> On Tue, Jul 5, 2011 at 8:12 PM, snoze pa <snoze.pa_at_gmail.com> wrote:
> > After many tweaks, the scripts start working. I will highly appreciate
> if
> > you can find if it is fine to do this way. If yes then in case of
> multiple
> > chains (chain A and chain B with same residue number) then how can I
> change
> > ths script.
>
> just figure out which index those atoms are
> beforehand and then use a selection "index #"
> this will certainly only get one atom.
> since you your atom indices won't change,
> you only have to do that once per system.
>
> >
> > Thank you.
> >
> > source bigdcd.tcl
> >
> > proc myrmsd { frame } {
> > global ref sel all
> > $all move [measure fit $sel $ref]
>
> why this?? $sel and $ref and $all
> are all the same molecule. thus the $all move
> won't change the distance between $sel and $ref
>
> > $sel frame $frame
> > $ref frame $frame
>
> if you update the frame here, the
> measure fit from above will be for
> the previous step.
>
> > set com1 [measure center $sel weight mass]
> > set com2 [measure center $ref weight mass]
>
> why measure center for a single atom??
>
> set coord1 [lindex [$sel get {x y z}] 0]
> set coord2 [lindex [$ref get {x y z}] 0]
>
> should do the same thing.
>
> > set comdist [vecdist $com1 $com2]
> > puts "$frame: $comdist"
> > }
> >
>
> axel.
>
> > set mol [mol new solvated_ionised.psf waitfor all]
> > set all [atomselect $mol all]
> > set ref [atomselect $mol "protein and resid 13 and name CA "]
> > set sel [atomselect $mol "protein and resid 18 and name CA "]
> >
> > mol addfile solvated_ionised.pdb type pdb waitfor all
> > bigdcd myrmsd dcd solvated_ionised4.dcd solvated_ionised5.dcd
> > bigdcd_wait
> > #quit
> >
> >
> > On Tue, Jul 5, 2011 at 6:12 PM, snoze pa <snoze.pa_at_gmail.com> wrote:
> >>
> >> Dear VMD users,
> >>
> >> I need some help to calculate the distance between atoms. I am using
> >> multiple large dcd files and would appreciate your help to get the
> corrected
> >> distance between two CA atoms of residue 13 and 18 along trajectory. I
> want
> >> to use bigdcd because large multiple dcd files. I am not expert in tcl
> >> programming but trying hard to get it.
> >>
> >> Thank you.
> >>
> >>
> >> source bigdcd.tcl
> >>
> >> proc myrmsd { frame } {
> >> global ref sel all
> >> $all move [measure fit $sel $ref]
> >> puts "$frame: [measure bond [list [list $ind1 $mol] [list $ind2
> $mol]]
> >> frame all]"
> >> }
> >>
> >> set mol [mol new solvated_ionised.psf waitfor all]
> >> set all [atomselect $mol all]
> >> set ref [atomselect $mol "protein and resid 13 and name CA"]
> >> set sel [atomselect $mol "protein and resid 18 and name CA"]
> >> set ind1 [join [$ref get index]]
> >> set ind2 [join [$sel get index]]
> >>
> >>
> >> mol addfile solvated_ionised.pdb type pdb waitfor all
> >> bigdcd myrmsd dcd solvated_ionised4.dcd solvated_ionised5.dcd
> >> bigdcd_wait
> >> #quit
> >>
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>