From: Kshatresh Dutta Dubey (kshatresh_at_gmail.com)
Date: Sun Dec 14 2014 - 14:52:54 CST

Hi,

Thanks a lot for your help. It works fine.

Regards
Kshatresh

On Sun, Dec 14, 2014 at 10:35 PM, Josh Vermaas <vermaas2_at_illinois.edu>
wrote:
>
> Hi Kshatresh,
>
> You need an "and" in between the water and the within 3 of resname HEM.
> The atomselection language just uses logical operations. The "water" refers
> to a macro that selects water molecules, which needs to be combined with a
> logical and with the selection of "within 3 of resname HEM". You also have
> some other elements in your script that may cause problems: a list
> operation when you try to write it out to the file that probably won't do
> what you expect. Here is what I would use for your script:
>
> set outfile [open waters.dat w];
> set nf [molinfo top get numframes]
> #I don't know if this matters to you, but I usually think its more useful
> to count by molecule rather than #by atom. This selection will only include
> water oxygen atoms that are in the same residue of #something within 3 of
> resname HEM.
> set sel [atomselect top "noh and water and same residue as within 3 of
> resname HEM"]
> for {set i 0 } {$i < $nf } { incr i } {
> $sel frame $i
> #The number of water molecules nearby will change, so the selection
> needs to change with the frame
> $sel update
> puts $outfile "$i [$sel num]"
> }
> close $outfile
>
> -Josh Vermaas
>
>
> On 12/14/2014 10:02 AM, Kshatresh Dutta Dubey wrote:
>
> Hi,
>
> I want to analyze the number of water molecules/per frame within some
> cutoff distance of residue of my simulated trajectories. I dont have
> expertise of tcl scripting however I tried following scripts:
>
> set outfile [open waters.dat w];
> set nf [molinfo top get numframes]
> set frame0 [atomselect top "water within 3 of resname HEM" frame 0]
> set sel [atomselect top "water within 3 of resname HEM"]
> for {set i 1 } {$i < $nf } { incr i } {
> $sel frame $i
> puts $outfile "[[ $sel $frame0] num] "
> }
> close $outfile
>
> But every time it is stops with error: atomselection: improper method:
> atomselect28, that means something is not right in last 3rd line.
> I will be thankful if someone suggests me to figure out the issue.
>
> Regards
> Kshatresh
>
>
>
>
>

-- 
With best regards
************************************************************************************************
Kshatresh Dutta Dubey
Post Doctoral Researcher,
Lise Meitner Center for Computational Quantum Chemistry
Hebrew University of Jerusalem Israel
Jerusalem, Israel