From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon May 05 2014 - 05:16:47 CDT

set frames [molinfo top get numframes]

set fp [open "waters.txt" w]

set ligand "resid 1 to 5"

 

for {set i 0} {$i < $frames} {incr i} {

                puts "Frame: $i"

                set a [atomselect top "(water within 5 of ($ligand)) and
oxygen"]

                set num [$a num]

                puts $fp "$i $num"

                $a delete

}

 

close $fp

 

Or similar .

 

Norman Geist.

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von
Ramin Ekhteiari
Gesendet: Montag, 5. Mai 2014 10:47
An: VMD Mailing List
Betreff: vmd-l: number of water molecules within 5 angstroms of the ligand

 

Hi dear all,

 

I would like to calculate number of water molecules within 5 angstroms of
the ligand

which is bonded to the protein for each step during MD.

I tried to do it for one step, but not for all as loop at TCL.

 

So would you please advise me on how to do it.

 

Would be grateful for any advice.

 

 

Cheers,

Ramin.

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