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<DIV><FONT size=2 face=Arial><SPAN class=796151712-13072011>Dear
all,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796151712-13072011>once again about
this subject (I'm not sure I'll do another simulation in a rhombic dodecahedron
system...)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796151712-13072011>I used g_sas to
compute solvent accessible surface area of my system. The command
was:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796151712-13072011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796151712-13072011>g_sas -f
prot_boxdodfull_mol.xtc -s prot_boxdodfull_molrenum.gro -o
prot_boxdodfull_sas.xvg -or prot_boxdodfull_sasres</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796151712-13072011>selecting 1
(protein) for calculation and for output.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796151712-13072011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796151712-13072011>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.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796151712-13072011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796151712-13072011>In addition, there
was another comment: No .tpr file, will not compute Delta G of solvation.
</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796151712-13072011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796151712-13072011>However, I tried to
do my calculation.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796151712-13072011>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.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796151712-13072011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=796151712-13072011>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...</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=796151712-13072011>Anna</SPAN></FONT></DIV>
<DIV> </DIV>
<DIV align=left>
<DIV dir=ltr align=left><FONT size=2
face=Arial>__________________________________________________________________</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Anna Marabotti, Ph.D.</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Laboratory of Bioinformatics and
Computational Biology</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Institute of Food Science -
CNR</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Via Roma, 64</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>83100 Avellino</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Phone: +39 0825 299651</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Fax: +39 0825 781585</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>E-mail: <A
title=mailto:amarabotti@isa.cnr.it
href="mailto:amarabotti@isa.cnr.it">amarabotti@isa.cnr.it</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Skype account: annam1972</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Web site: <A
title=http://bioinformatica.isa.cnr.it/anna/anna.htm
href="http://bioinformatica.isa.cnr.it/anna/anna.htm">http://bioinformatica.isa.cnr.it/anna/anna.htm</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial></FONT> </DIV>
<DIV align=left><FONT size=2 face=Arial>"When a man with a gun meets a man with
a pen, the man with the gun is a dead man"</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>(Roberto Benigni, about Roberto
Saviano)</FONT></DIV></DIV>
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