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: amarabo...@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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