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

[ozge engin]

Thank you very much Anthony,I will try it!

Ozge

----- Original Message ----- 
From: "Anthony Cruz Balberdi" <acb15885 at uprm.edu>
To: <OZENGIN at ku.edu.tr>
Cc: <gmx-users at gromacs.org>
Sent: Monday, March 19, 2007 3:19 PM
Subject: Re: [gmx-users] Appropriate tool to get the number of
solventmolecules within a cutoff distance around protein molecule


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 <OZENGIN at KU.EDU.TR> 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



_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php



-------------------------------------------------------------
Antes ahora y siempre COLEGIO
University of Puerto Rico at Mayaguez
http://www.uprm.edu
-------------------------------------------------------------


_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php