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
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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