VMD-L Mailing List

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Mon Mar 06 2006 - 10:20:08 CST

Hi:
I want to do something like that and with the help of John Stone
<johns_at_ks.uiuc.edu> I made the following script:

################################
set outfile [open sol_in.dat w];
set nf [molinfo top get numframes]
set frame0 [atomselect top "protein" frame 0]
# inside water calculation loop
for {set i 1 } {$i < $nf } { incr i } {
    set prot [atomselect top "protein" frame $i]
    $prot move [measure fit $prot $frame0]
    set rg [measure rgyr $prot]
    set com [measure center $prot weight mass]
    set xcom [lindex $com 0]
    set ycom [lindex $com 1]
    set zcom [lindex $com 2]
    set r2 [expr $rg*$rg]
    set sol2keep [atomselect top "(same residue as
((sqr(x-$xcom)+sqr(y-$ycom)+sqr(z-$zcom)) <= $r2)) and resname water"]
#1set sol2keep [atomselect top "(same residue as
((sqr(x-$xcom)+sqr(y-$ycom)+sqr(z-$zcom)) <= $r2)) and type OW"]
    set nummolP [$sol2keep num]
    set nummolR [expr $nummolP/3]
    puts $outfile "$i $nummolR"
#2 puts $outfile "$i $nummolP"
}
close $outfile
##################################

the script calculate the Rg of the protein and the center of mass then it
makes a selection of all molecules of water that have a distance from the
center of mass that is iqual or less that the Rg^2 then divide the number of
atoms in de selection by 3 resulting in the corresponding number of water in
the section. Or if you want you could uses the lines that have the #1 and #2
and have the number of water directly write to the file. I hope that this
help you

Best regards
Anthony

On Wednesday 01 March 2006 3:44 pm, John Stone wrote:
> Hi,
> So you're looking for a script to identify "buried" atoms, or
> waters in internal cavities? Finding buried protein atoms might
> be doable by selecting atoms with near-zero SASA values, the inverse
> of what someone else just asked for. Finding buried waters would
> require some trickery, perhaps you could calculate the SASA values
> for waters within a cutoff of "protein", and then sift through those
> finding atoms with near-zero SASA values. That may or may not work,
> but it's an idea to start with.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Mar 01, 2006 at 12:50:00AM +0000, ziemys_at_ecr6.ohio-state.edu wrote:
> > Hi,
> >
> > How to select atoms (e.g. water molecules) inside protein (within protein
> > volume) ?
> >
> > With best
> > Arturas