AMBER Archive (2008)

Subject: Re: AMBER: ptraj - closest command

From: sobereva (sobjubao_at_yahoo.com.cn)
Date: Wed Oct 08 2008 - 21:49:46 CDT

Hi,

I think it is hard to use ptraj for solving your
problem.
I suggest you to use VMD Tcl command,it's more
powerful.
For example,you want to get the number of waters lying
in 5 angstrom of residue 15,your trajectory has 200
frames,input below into VMD Tk console.

for {set i 0} {$i<200} {incr i 1} {
atomselect top {same residue as{waters within 5 of
resid 15}} frame $i
puts "Frame: $i number of waters: [expr [atomselect$i
num]/3]"
}

Then output like this:
......
Frame: 196 number of waters: 14
Frame: 197 number of waters: 13
Frame: 198 number of waters: 13
Frame: 199 number of waters: 12

You can change the script as you want,please refer to
VMD userguide.

--- Ryan Pavlovicz <pavlovicz.7_at_osu.edu> wrote:

> I figured out my initial problem: i was using
> 'trajectory smoothing' when
> viewing the trajectory in VMD. Because the residues
> essentially change
> identity when they leave and then reenter the 50
> water sphere, this messes
> up the smoothing and therefore my visualization of
> the solvation. I don't
> think the order in which i used the 'image' command
> had an effect on this,
> since 'closest' automatically images the waters
> before the distance
> calculations.
>
> So now, what i would really like to do is figure out
> the residue numbers of
> the waters that come within a specific radius of a
> mask. Can ptraj do
> this? This way i could then strip all but the
> waters i am interested then
> get better tracking of the waters of interest when
> viewing the trajectory in
> VMD. I have previously done something similar to
> this with the
> ''atomicfluct byres" command to sort the more stable
> waters from the more
> mobile ones. While this allows me to get the
> numbers of most of the waters
> that i am interested in, since they are stable in
> the binding pocket, a few
> of the more transient waters are missed.
>
> thanks again,
>
> -ryan
>
> On Wed, Oct 8, 2008 at 3:50 PM, Jianyin Shao
> <jyshao2004_at_gmail.com> wrote:
>
> >
> >
> > On Wed, Oct 8, 2008 at 11:36 AM, Ryan Pavlovicz
> <pavlovicz.7_at_osu.edu>wrote:
> >
> >> Hi. I am trying to visualize an explicitly
> solvated MD trajectory to
> >> analyze waters in a protein active site. Since
> it is very difficult and
> >> CPU-intensive to visualize all of the waters in
> the entire system, i would
> >> like to strip all waters but for those that enter
> the binding pocket. It
> >> seems that the ptraj command 'closest' more or
> less should do what i want.
> >> I tried to keep the closest 50 waters to an atom
> of interest:
> >>
> >> closestwater 50 :15_at_SG oxygen
> >>
> >> Then i create a new prmtop file that has my
> protein in addition to 50
> >> waters, but the visualization in VMD seems
> incorrect. While all of the
> >> waters are surrounding the area of interest, many
> of the waters i am viewing
> >> seem to be intersecting each other or coming
> unreasonably close to the
> >> protein. Here is the entire script i am using:
> >>
> >> #!/bin/bash
> >> ptraj in.prmtop << EOF
> >> trajin in.crd
> >>
> >> closestwater 50 :15_at_SG oxygen
> >> image :WAT byres
> >> rms first mass :13-146_at_CA,C,N:176-309_at_CA,C,N
> >> trajout in_trajout.crd
> >>
> >> go
> >> EOF
> >>
> >> Can any one spot a problem, suggest a fix, or
> suggest an alternate method
> >> to preserve the waters that enter the active site
> while stripping the
> >> others? Thanks.
> >>
> >
> > I think you should do "image" command before the
> "closestwater" command.
> > Best,
> >
> > Jianyin
> >
>

-- Lu Tian
Institute of Chemistry
Beijing Normal University
No.19 XinJieKouWai Street,Beijing

      
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