[gmx-users] On the usage of g_sas

Justin Lemkul jalemkul at vt.edu
Tue Oct 8 13:59:09 CEST 2013

On 10/8/13 7:27 AM, Jernej Zidar wrote:
> Hi,
>    I would like to use g_sas to determine the surface properties of an
> organic molecule and was wondering whether to trust g_sas in picking the
> hydrophobic/hydrophilic atoms. I also saw one can supply an option index
> file -f_index) for that but nothing is said about the form of this file.
> Which option is better? I'm using the Charmm-generalized forcefield.

The index file taken by g_sas serves the function of any other Gromacs program; 
it allows you to choose special calculation and/or output groups.  It doesn't 
let you choose which atoms are hydrophobic or hydrophilic, AFAIK.  The choice is 
made based on the charges read in the .tpr file.  If |q| < 0.2, the atom is 
hydrophobic, otherwise it is hydrophilic.  If that choice doesn't suit you, you 
can either modify the code or create a fake topology (for the purpose of 
analysis only!) with different charges that lead to different assignments.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list