From: Christopher Gillespie (gillescche_at_gmail.com)
Date: Tue Jul 29 2008 - 18:39:14 CDT

Hello again,
Thank you Eduard and John for the help.

Using Eduard's suggestion for surface selection I modified my script to set
only protein atoms within 2.8A of water, updated at each frame. The problem
is that it takes until ~40A to get g(r) to 1, specifically g(r) is always <
1 until it nears 40A. I believe this is due to the averaging including the
shell area that is blocked by the rest of the protein atoms, i.e. the shel
volume should be less then 4*pi*r^2*dr to remove the volume occupied by the
protein. Has someone already tackled this issue.

If some one wants to see the g(r) plots I can forward them directly.

Thanks

Chris

gofr Script

 set sol [atomselect top "water and noh"] ;# Water selection

 set cat [atomselect top "name SOD"] ;# Sodium ions selection

 set ani [atomselect top "name CLA"] ;# Chloride ions selection

 set surf [atomselect top "same residue as protein and within 2.8 of water
and noh"]

 set dr 0.002 ;# bin size (Ang.) Shortened due to Axel Kohlmeyer's
recommendation

 set dim 40 ;# rdf Range (Ang.)

 set out1 [open gofrSurfWat.dat w] ;# Output file for water rdf

 set out2 [open gofrSurfNa.dat w] ;# Output file for sodium rdf

 set out3 [open gofrSurfCl.dat w] ;# Output file for chloride rdf

 set frm [molinfo top get numframes] ;# Determine number of loaded frames

 set i [expr $frm -1]

 puts " Number of frames to process : $i"

# Sodium

 puts ""

 puts "Starting with Sodium"

 set grN [measure gofr $surf $cat delta $dr rmax $dim usepbc 1 selupdate 1
first 1 last -1 step 1]

 set rN [lindex $grN 0]

 set gN [lindex $grN 1]

 foreach j $rN k $gN {

puts $out2 "$j $k"

 }

# Chloride

 puts ""

 puts "Now Chloride"

 set grC [measure gofr $surf $ani delta $dr rmax $dim usepbc 1 selupdate 1
first 1 last -1 step 1]

 set rC [lindex $grC 0]

 set gC [lindex $grC 1]

 foreach j $rC k $gC {

puts $out3 "$j $k"

 }

 # Water

 puts ""

 puts "Finally Water"

  set grO [measure gofr $surf $sol delta $dr rmax $dim usepbc 1 selupdate 1
first 1 last -1 step 1]

 set rO [lindex $grO 0]

 set gO [lindex $grO 1]

 foreach j $rO k $gO {

puts $out1 "$j $k"

 }

 puts " "

 puts "All Done"

 puts " "

On Mon, Jul 21, 2008 at 11:22 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Beyond the reply that Eduard already sent, I just wanted to mention
> that you can use a script to compute SASA per residue, assign the
> per-residue SASA to "beta" or "user" (Just as an example. You could
> just as easily use any of the per-atom fields) and then use a selection
> like:
> beta > 0
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sun, Jul 20, 2008 at 05:28:04PM -0400, Christopher Gillespie wrote:
> > Hello,
> > I am trying to generate some rdfs for systems that I have already run. I
> > want to do these using the protein surface as one selection. I know that
> > using the selection "Protein and Surface" only implies "Not Buried" which
> > removes hydrophobic residues from the selection set, but I want to see
> the
> > actual atoms, including any hydrophobic ones that have at least some
> SASA,
> > while also not including polar atoms that are actually buried, e.g. at
> the
> > dimer interface. I know it may not be exactly correct since I should
> have
> > to determine the SASA for each frame, but to make this doable in a
> > reasonable amount of time and since my protein has an average RMSD of
> ~1.2A
> > the atoms that make up the set from frame 0 should not deviate that much,
> I
> > assume.
> >
> > So does anyone know how to define a selection of SASA > 0 atoms for use
> in
> > gofr?
> >
> > Thanks
> >
> > Chris
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>