[gmx-users] rhombic dodecahedron and g_sas

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jul 13 15:54:07 CEST 2011

Hi Anna,

It would have been best if you provided us the exact output of g_sas.
In any case, the classification of your atoms has nothing to do with
the type of PBC. It has to do with the fact you're using a .gro file
as a reference, which contains no charges. As a consequence, all atoms
are taken to have zero charge, and thus regarded hydrophobic.



On Wed, Jul 13, 2011 at 2:35 PM, Anna Marabotti
<anna.marabotti at isa.cnr.it> wrote:
> 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
> appreciated...
> Anna
> __________________________________________________________________
> 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
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> (Roberto Benigni, about Roberto Saviano)
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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