[gmx-users] g_sas on pdb files

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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