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.
Cheers, Tsjerk On Wed, Jul 13, 2011 at 2:35 PM, Anna Marabotti <[email protected]> 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: [email protected] > 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) > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
