[gmx-users] Calculating the Hydrophobic and Hydrophilic SASA values on GROMACS version 5.1.2

[Dallas Warren]

http://manual.gromacs.org/documentation/5.1-current/onlinehelp/gmx-sasa.html

Appropriate use of index groups is what you need to do, separate out
the hydrophobic and hydrophilic groups/atoms, then pass the index
group via -n

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
On Wed, 5 Sep 2018 at 14:26, Andrew Srimalka Wijesekera
<2014s14712 at stu.cmb.ac.lk> wrote:
>
> Dear all,
>
> I'm currently studying the structural changes and thermodynamic properties
> of a protein structure when binding the ligand. Here I have ran the MD run
> for 50 ns and calculate the SASA value from the gromacs 5.1.2 version.
> According to my knowledge I got only the total SASA value. But I want to
> get the hydrophobic and hydrophilic SASA values seperately from the gromacs
> 5.1.2 version as well. Therefore would you please help me to solve this
> problem.
> Thanks in advance.
> --
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