[gmx-users] g_sas on pdb files

Justin Lemkul jalemkul at vt.edu
Tue Jun 18 13:56:36 CEST 2013

On 6/18/13 7:41 AM, erin.cutts wrote:
> I'm trying to compare the hydrophobic surface generated from my trajectory
> with g_sas to a range of random coil .pdb files with my protein sequence,
> but I can't figure out how to make the structure+mass input that is required
> for g_sas from my pdb files i.e. in the manual
> "Structure+mass(db): tpr tpb tpa gro g96 pdb"
> Just using the pdb file itself results in it not being able to define which
> residues are hydrophobic and it doesn't work. I want the two calculations to
> be as comparable as possible.
> Thanks for any help people can give.

Within g_sas, hydrophobicity is defined by the charge carried by each atom, and 
thus a .tpr file is required.  While not strictly necessary, I think it makes 
the result more reliable.  Otherwise, I believe g_sas defaults to guessing based 
on atom names.  For comparison purposes, that may work, but in terms of absolute 
figures, it may not be reliable.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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