Hi Ozge:
You can use a script in VMD to do the work. In VMD you could make various atom
selection and use it in the script. You
could use something like this:
set outfile [open sol_within_prot.dat w];
set nf [molinfo top get numframes]
set frame0 [atomselect top "protein" frame 0]
# 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 sol2keep [atomselect top "(same residue as (within 2 of protein)) and
resname SOL" frame $i]
set nummolP [$sol2keep num]
set nummolR [expr $nummolP/3]
puts $outfile "$frame $nummolR"
puts "$frame"
}
close $outfile
Probably you will need to fit your trajectory if your protein go near the edge
of the box
because VMD does not take in account the PBC in this type of calculation.
Anthony
OZGE ENGIN <[EMAIL PROTECTED]> wrote:
Hi,
I want to calculate the number of solvent molecules within a cutoff distance
around the protein molecule. I could not
find the appropriate command for this in manual. Moreover, I could not
understand the information for g_sorient.Could
you give me a more detailed explanation for this?
Thanks in advance
Ozge Engin
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Antes ahora y siempre COLEGIO
University of Puerto Rico at Mayaguez
http://www.uprm.edu
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