[gmx-users] On the usage of g_sas
jalemkul at vt.edu
Tue Oct 8 13:59:09 CEST 2013
On 10/8/13 7:27 AM, Jernej Zidar wrote:
> 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.
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
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