[gmx-users] On the usage of g_sas

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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