On 2010-04-04 07.13, Chih-Ying Lin wrote:
HI
THe command =>
g_sas_mpi -f 6LYZ-MD566500.xtc -s 6LYZ-MD566500.tpr -o
solvent-accessible-surface.xvg -oa atomic-sas.xvg -or residue-sas.xvg
In the solvent-accessible-surface.xvg =>
@ s0 legend "Hydrophobic"
@ s1 legend "Hydrophilic"
@ s2 legend "Total"
@ s3 legend "D Gsolv"
What does "Hydrophobic" mean here?
What does "Hydrophilic" mean here?
Does "Total = Hydrophobic+Hydrophilic" ?
What does "D Gsolv" mean here?
How can Gromacs define "Hydrophobic atoms" and "Hydrophilic atoms" ?
DG solv is computed according to Eisenberg et al. See scree output for
reference.
Hydrophobicity is determined from the charge of an atom, not a very good
method maybe, there you can supply an index file to determine which
residues are hydrophobic yourself.
What does the Area unit mean ? => "Area (nm\S2\N)"
How about square nanometer for an area?
Thank you
Lin
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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