[gmx-users] Re:On the usage of g_sas

Jernej Zidar jernej.zidar at gmail.com
Wed Oct 9 04:39:51 CEST 2013

Dear Justin,
  Thanks for the help.

  That's what the manual says about the "-f_index" switch:
"Determine from a group in the index file what are the hydrophobic
atoms rather than from the charge"

What confuses me is that this is the only thing related to the matter,
no word about the naming conventions. Even ol' fella Google can't find
anything related to this issue.


> 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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