[gmx-users] rhombic dodecahedron and g_sas

Anna Marabotti anna.marabotti at isa.cnr.it
Wed Jul 13 14:35:56 CEST 2011

Dear all,
once again about this subject (I'm not sure I'll do another simulation in a
rhombic dodecahedron system...)
I used g_sas to compute solvent accessible surface area of my system. The
command was:
g_sas -f prot_boxdodfull_mol.xtc -s prot_boxdodfull_molrenum.gro -o
prot_boxdodfull_sas.xvg -or prot_boxdodfull_sasres
selecting 1 (protein) for calculation and for output.
I saw the following Warning message: non-rectangular boxes may give
erroneous results or crashes. Analysis based on vacuum simulations (with the
possibility of evaporation) will certainly crash the analysis.
In addition, there was another comment: No .tpr file, will not compute Delta
G of solvation. 
However, I tried to do my calculation.
At the start, I saw a message saying that all the atoms of my protein were
classified as hydrophobic (that is indeed a very strange behaviour; my
protein is a globular protein, and certainly not all their atoms are
hydrophobic). At the end of calculation, looking at the .xvg file with
xmgrace -nxy, I saw indeed that hydrophobic and total SASA coincide, whereas
the hydrophilic area is 0 for all the time.
I think this is an artifact of the non-rectangular box. Am I true? What can
I do? Do I have to convert my trajectory into a rectangular one? Do I have
to forgot to calculate SASA in these conditions? Any help will be
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science - CNR
Via Roma, 64
83100 Avellino
Phone: +39 0825 299651
Fax: +39 0825 781585
E-mail: amarabotti at isa.cnr.it
Skype account: annam1972
Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
"When a man with a gun meets a man with a pen, the man with the gun is a
dead man"
(Roberto Benigni, about Roberto Saviano)
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