[gmx-users] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule

Anthony Cruz Balberdi acb15885 at uprm.edu
Mon Mar 19 14:19:00 CET 2007

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. 



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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