[gmx-users] g_sas on pdb files

erin.cutts erin.cutts at wolfson.ox.ac.uk
Tue Jun 18 13:41:08 CEST 2013

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.


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