Re: vmd-l: water molecules around proteins

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Mar 11 2010 - 11:49:50 CST

On Thu, 2010-03-11 at 12:40 -0500, Florentina Tofoleanu wrote:
> Thank you Axel for your answer. I added that line,
>
> pbc wrap -molid $mol -compound res -centersel $refA -first $frame
> -last $frame
>
> but I get this error:
>
> -error Suspicious pbc side length (a=0.000000 b=0.000000 c=0.000000).
> Have you forgotten to set the pbc parameters?
> domain error: argument not in valid range

this means, that one of more frames of your .dcd file have
no information about the size of your simulation cell.
btw, this would also cause problems in the case of using
a selection containing "pbwithin".

check out the pbctools plugin documentation on how to
print, read, and apply cell size information using pbctools.

cheers,
    axel.

>
> Only "pbc wrap -molid $mol -compound res -centersel $refA" works fine,
> but just for the last frame. I wrote this little script to get the
> result only for the "wrap" function. Could you explain me why it
> doesn't change all the frames even though it is in a "for" cycle? Is
> it related to the inutility of "$refA frame $frame", being the same
> selection in every frame you need to specify the frames you want to
> change?
>
> set mol [mol new file.psf type psf waitfor all]
> mol addfile file.dcd type dcd waitfor all molid $mol
>
> set numframes [molinfo $mol get numframes]
> set all [atomselect top all]
> set refA [atomselect $mol "protein"]
>
> for {set frame 0} {$frame < $numframes} {incr frame} {
>
> #$refA frame $frame
>
> pbc wrap -molid $mol -compound res -centersel $refA
> #pbc wrap -molid $mol -compound res -centersel $refA -first $frame
> -last $frame
>
> animate write dcd wrap.dcd sel $all
> }
>
> Could you tell me what I need to change to make it work?
>
> Regards,
>
> Florentina
>
> On Wed, Mar 10, 2010 at 6:41 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> On Wed, Mar 10, 2010 at 5:27 PM, Florentina Tofoleanu
> <florentina.tofoleanu_at_gmail.com> wrote:
> > Hello,
>
> hi florentina,
>
> [...]
>
> > $refA update
>
> this update is not really needed. this selection will not
> change.
>
> > $refB update
> >
> > set nhb [llength [lindex [measure hbonds 3.1 60 $refA $refB]
> 0]]
>
>
> here is the culprit. while $refB will select positions with
> PBC in mind,
> it actually does not include multiple copies of the
> coordinates and thus
> measure hbonds will only compute the distances to the original
> coordinates of all particles. i.e. it is not PBC aware and
> thus you
> get in both cases the same result.
>
> if you cell is large enough, you might want to try running
> pbc wrap with providing $refA (or rather its center of mass)
> as the reference point for the center of the wrapping.
> this way your "within" selection should be ok.
>
> >
> > puts $outfile "$frame $nhb"
> >
> > }
> >
> > close $outfile
> >
> >
> > Is there an error in the script, or just the pbwithin
> command won't do?
> >
> > I've seen in this post
> >
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14664.html
> > "(Pbwithin) does not, however, modify the coordinates - they
> will still be
> > the coordinates of the atom in the primary image, so if you
> want to compute
> > distances, you need to take into account the periodic
> boundary conditions
> > manually. " Could Olaf, or anybody else, explain what taking
> into account
> > the pbc manually mean and how can I change my script?
>
>
> how about adding?
>
> pbc wrap -molid $mol -compound res -centersel $refA -first
> $frame -last $frame
>
> (add -orthorhombic for more speed, if your cell is
> orthorhombic)
>
> cheers,
> axel.
>
>
> >
> > Thank you,
> >
> > Florentina
> >
> >
> > On Sat, Sep 19, 2009 at 9:55 AM, Axel Kohlmeyer
> <akohlmey_at_gmail.com> wrote:
> >>
> >> 2009/9/19 Thomas Evangelidis <te8624_at_mbg.duth.gr>:
> >> > Hi Katherine,
> >> >
> >> > lets say you want to count all the waters(TIP3) within 5
> A of resids
> >> > 1-50
> >> > taking into account waters in the nearest periodic cells,
> then the
> >> > command
> >> > should be:
> >> >
> >> > llength [[atomselect top "(oxygen pbwithin 5 of (protein
> and resid 1 to
> >> > 50))
> >> > and resname TIP3"] list]
> >>
> >> folks,
> >>
> >> when giving code examples, please make sure that you give
> examples
> >> of _good_ coding. this piece of code has a high risk of
> creating a memory
> >> leak
> >> and is inefficient.
> >>
> >> the same can be done by:
> >>
> >> set sel [atomselect top "(oxygen pbwithin 5 of (protein and
> resid 1 to
> >> 50)) and resname TIP3"]
> >> puts "found [$sel num] water molecules"
> >> $sel delete
> >>
> >> and this code uses the "num" option to do the counting in c
> rather
> >> than creating a tcl
> >> list and counting its length and show that the functions
> created by
> >> atomselect have to
> >> be deleted after use (it is better to always manually
> delete them
> >> rather than counting
> >> on tcl to clean up).
> >>
> >> > I have an alpha version of a plugin to truncate
> trajectories and keep
> >> > only a
> >> > specified number of waters within R Angstroms of an
> atomselection, it
> >> > might
> >> > be helpful to your analysis.
> >>
> >> that reminds me. having you been able to sort out your
> issues with bigdcd?
> >> did the improved re-rentrant version of bigdcd work for
> you?
> >>
> >>
> >> thanks,
> >> axel.
> >> >
> >> > regards,
> >> > Tom
> >> >
> >> >
> >> >> Dear VMD users:
> >> >> My sytem contains 18 proteins in a unit cell. I also
> have several 20ns
> >> >> trajectories (*.dcd) of this system.
> >> >> I would like to calculate the distribution of the water
> molecules
> >> >> around
> >> >> each one of the proteins and around the different
> amoinoacids that
> >> >> compose
> >> >> them during the trajectories.
> >> >> I've been trying to find another VMD mail list posted
> message
> >> >> containing
> >> >> this question and somewhere in the VMD user's guide but
> I haven't found
> >> >> anything related.
> >> >> I've worked with some scripts in VMD, using the
> atomselect command and
> >> >> doing
> >> >> loops along trajectories.
> >> >> What I need is some help with the right command to count
> water
> >> >> molecules
> >> >> (TIP3) around a specific part of the protein.
> >> >> Thank you in advance.
> >> >> KP
> >> >>
> >> >
> >> >
> >> > ----- End message from kparra_at_mail.usf.edu -----
> >> >
> >> >
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> >> Institute for Computational Molecular Science
> >> College of Science and Technology
> >> Temple University, Philadelphia PA, USA.
> >
> >
> >
> > --
> > Florentina Tofoleanu
> > Postgraduate Research Fellow
> > Theoretical and Computational Biophysics Group
> > University College Dublin
> > School of Physics, Rm. 110
> > Belfield, Dublin 4, Ireland
> >
>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
>
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
>
>
> Temple University, Philadelphia PA, USA.
>
>
>
>
> --
> Florentina Tofoleanu
> Postgraduate Research Fellow
> Theoretical and Computational Biophysics Group
> University College Dublin
> School of Physics, Rm. 110
> Belfield, Dublin 4, Ireland

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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