Hey,

I typically use

http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-sasa.html

It‘s the gromacs program to calculate that where you can choose from a range of parameters.

Best

Otto

I have used the 'measure sasa' function in VMD for many years and it works well for me.

I think the problem might be related to your selections. Also, I am not sure what you want to measure. You want to measure the SASA of a single water molecule in a solution containing many water molecules?

Which atoms/molecules do the selections $all and $sel refer to?

It might be useful to add the option '-points varname' to the sasa command for visualization of the measured surface area. This stores the surface area as the variable 'varname' which can be visualized using the command:

foreach pt $varname {

draw point $pt

}

Hello Christian Schönbeck

I want to measure the SASA of a single water molecule.

I have tried to change the $all as water and $sel as my water number (e.g. W1234)

It is giving me a positive output instead of just zero. However i am not sure whether this command is correct or not.

I have attach the sasa.tcl command.

puts -nonewline "\n \t \t Selection: "

gets stdin selmode

# selection

set sel [atomselect top "$selmode"]

set water [atomselect top "water"]

set n [molinfo top get numframes]

set output [open "SASA_$selmode.dat" w]

# sasa calculation loop

for {set i 0} {$i < $n} {incr i} {

molinfo top set frame $i

set sasa [measure sasa 1.4 $water -restrict $sel]

puts "\t \t progress: $i/$n"

puts $output "$sasa"

}

puts "\t \t progress: $n/$n"

puts "Done."

puts "output file: SASA_$selmode.dat"

close $output

Alvea Tasneem I think I see the problem. $water is a selection of all water molecules and $sel is the particular water molecular for which you want to measure SASA, right?

What your command 'measure sasa 1.4 $water -restrict $sel' does is that it considers all of the water as one big entity but it only measures the part of that big entitys surface area that is defined as $sel. This means that whenever your $sel water molecule is at the surface of the water box you will get a positive number. Whenever your $sel water molecule is buried inside the water box you will get 0.0.

Solving your problem requires only a slight simplification. You don't need to use the -restrict option. Just change the command line:

set sasa [measure sasa 1.4 $water -restrict $sel]

to

set sasa [measure sasa 1.4 $sel]

I hope this solves your problem.

Btw, the VMD User's guide provides additional information on how to use sasa.

http://www.ks.uiuc.edu/Research/vmd/current/docs.html

Christian Schönbeck I have tried using your simplified script. It is giving me higher value as compared to what i was getting with -restrict $sel script.

set sel [atomselect top "resid 3058"]

set sasa [measure sasa 1.4 $sel]

The result was 104.05859375.

And mine was with -restrict $sel and $water was 38.90548324584961

SO now i am confuse which value is better.

For your consideration i am attaching my protein.pdb file which is the last frame of 100ns MD simulation. I have measure the sasa value of some selected water molecules such as W3058.

I hope it will help you to better understand my problem.

Thank you in advance.