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

Dallas Warren dallas.warren at monash.edu
Wed Sep 5 06:35:44 CEST 2018


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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