<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV id=yiv674119952>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman" size=3>Dear Sir, </FONT>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt; TEXT-ALIGN: justify"><FONT size=3><FONT face="Times New Roman"><SPAN> </SPAN><SPAN> </SPAN>I am facing one problem regarding generation of Free energy landscape (FEL); I have some doubt regarding the algorithm of g_sham. I will be highly obliged if you kindly let me clear my doubt. I know that three variables are needed for construction of 3D energy landscape.<I> </I><SPAN>The free energy = -KBTln(probability of conformational distribution). But I can not understand how to find the conformational distribution, is it already embedded in the algorithm of g_sham?</SPAN></FONT></FONT>
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<P class=MsoNormal style="MARGIN: 0in 0in 0pt; TEXT-ALIGN: justify"><FONT face="Times New Roman" size=3>I followed the following procedure mentioned below.</FONT>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt; TEXT-ALIGN: justify"><FONT face="Times New Roman" size=3> </FONT>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt; TEXT-ALIGN: justify"><FONT size=3><FONT face="Times New Roman">First I prepared an xvg file with 3 columns; the first is the time frame, 2<SUP>nd</SUP> and 3<SUP>rd</SUP> parameters are the parameters I want to calculate, for eg the projections along 1<SUP>st</SUP> and 2<SUP>nd</SUP> Principal Components.<SPAN> </SPAN></FONT></FONT>
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<P class=MsoNormal style="MARGIN: 0in 0in 0pt; TEXT-ALIGN: justify"><FONT size=3><FONT face="Times New Roman">Then I used the command<SPAN> </SPAN></FONT></FONT>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt; TEXT-ALIGN: justify"><FONT face="Times New Roman" size=3>g_sham –f<SPAN> </SPAN>*.xvg <SPAN> </SPAN>-ls </FONT>
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<P class=MsoNormal style="MARGIN: 0in 0in 0pt; TEXT-ALIGN: justify"><FONT face="Times New Roman" size=3>Then I converted gibbs.xpm into an eps file using xpm2ps –rainbow. The file that I obtained is not showing free energy landscape, rather an eps file is generated which contains some scattered square like conformations. Please suggest If I am doing anything wrong. Should I follow the same procedure while generating the FEL using other variables like potential energy, Rg or RMSD? </FONT>
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<P class=MsoNormal style="MARGIN: 0in 0in 0pt; TEXT-ALIGN: justify"><FONT face="Times New Roman" size=3>It may be a silly question, but I am a new comer in this field, so please bear with me. Your urgent help in this matter is highly appreciated. </FONT>
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<P class=MsoNormal style="MARGIN: 0in 0in 0pt; TEXT-ALIGN: justify"><FONT face="Times New Roman" size=3> </FONT>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt; TEXT-ALIGN: justify"><FONT face="Times New Roman" size=3>Regards</FONT>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt; TEXT-ALIGN: justify"><FONT face="Times New Roman" size=3>Sangeeta</FONT></DIV></DIV></td></tr></table><br>
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