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<P class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: 12.5pt"><SPAN style="FONT-SIZE: 7pt; FONT-FAMILY: SimSun"><FONT size="5"><SPAN style="mso-spacerun: yes"><SPAN style="FONT-FAMILY: SimSun"><FONT size="3">Dear All,</FONT></SPAN></SPAN></FONT></SPAN></P>
<P class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: 12.5pt"><SPAN style="FONT-SIZE: 7pt; FONT-FAMILY: SimSun"><FONT size="5"><SPAN style="mso-spacerun: yes"><SPAN style="FONT-FAMILY: SimSun"><FONT size="3"><o:p></o:p></FONT></SPAN> </SPAN></FONT></SPAN></P>
<P class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: 150%"><SPAN style="FONT-FAMILY: SimSun"><FONT size="3"> I have make a free energy landscape by using the data of RMSD and H-bond number of main chain of a protein according to the following method. I am not sure if the method does work. If not, Could you give me some advises? Thank you!</FONT></SPAN></P>
<P class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: 150%"><SPAN style="FONT-FAMILY: SimSun"><FONT size="3">PS: Method</FONT></SPAN></P>
<P class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: 150%"><SPAN style="FONT-FAMILY: SimSun"><FONT size="3"> 1. Obtained the RMSD and the number of H-bond of mainchain of the protein by using g_rms and g_hbond commonds;<o:p></o:p></FONT></SPAN></P>
<P class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: 150%"><SPAN style="FONT-FAMILY: SimSun"><FONT size="3"> 2. Copy above two groups of values (RMSD and H-bond number) into Origin Software. first column is values of H-bond number, second column is RMSD;<o:p></o:p></FONT></SPAN></P>
<P class="MsoNormal" style="MARGIN: 0in 0in 0pt; TEXT-INDENT: 14.25pt; LINE-HEIGHT: 150%"><SPAN style="FONT-FAMILY: SimSun"><FONT size="3">3. Statistics > Descriptive Statistics > 2D Frequency Count in Origin, and obtained a matrix named as"TwoD FreqCounts";<o:p></o:p></FONT></SPAN></P>
<P class="MsoNormal" style="MARGIN: 0in 0in 0pt; TEXT-INDENT: 14.25pt; LINE-HEIGHT: 150%"><SPAN style="FONT-FAMILY: SimSun"><FONT size="3">4. Convert the above matrix into worksheet with type of xyz, and<SPAN style="mso-spacerun: yes"> </SPAN>got the values in the third column (frequency counts of RMSD and H-bond number);<o:p></o:p></FONT></SPAN></P>
<P class="MsoNormal" style="MARGIN: 0in 0in 0pt; TEXT-INDENT: 14.25pt; LINE-HEIGHT: 150%"><SPAN style="FONT-FAMILY: SimSun"><FONT size="3">5. Calculate the frequency count into normalized possibility;<o:p></o:p></FONT></SPAN></P>
<P class="MsoNormal" style="MARGIN: 0in 0in 0pt; TEXT-INDENT: 14.25pt; LINE-HEIGHT: 150%"><SPAN style="FONT-FAMILY: SimSun"><FONT size="3">6. Select the maximal or minimal possibility as control value.<o:p></o:p></FONT></SPAN></P>
<P class="MsoNormal" style="MARGIN: 0in 0in 0pt; TEXT-INDENT: 14.25pt; LINE-HEIGHT: 150%"><SPAN style="FONT-FAMILY: SimSun"><FONT size="3"><SPAN style="mso-spacerun: yes"> </SPAN>If<SPAN style="mso-spacerun: yes"> </SPAN>you select the maximal possibility (Pmax) as control value, the ΔG = G<SUB>x</SUB> - G<SUB>max</SUB> = -k<SUB>B</SUB>Tln(Px/Pmax) > 0;<o:p></o:p></FONT></SPAN></P>
<P class="MsoNormal" style="MARGIN: 0in 0in 0pt; TEXT-INDENT: 14.25pt; LINE-HEIGHT: 150%"><SPAN style="FONT-FAMILY: SimSun"><FONT size="3"><SPAN style="mso-spacerun: yes"> </SPAN>If<SPAN style="mso-spacerun: yes"> </SPAN>you select the minimal possibility (Pmin) as control value, the ΔG = G<SUB>x</SUB> - G<SUB>min</SUB> = -k<SUB>B</SUB>Tln(Px/Pmin) < 0;<o:p></o:p></FONT></SPAN></P>
<P class="MsoNormal" style="MARGIN: 0in 0in 0pt; TEXT-INDENT: 14.25pt; LINE-HEIGHT: 150%"><SPAN style="FONT-FAMILY: SimSun"><FONT size="3">Calculate all the values of (Px/Pmax) or (Px/Pmin) as the new third column. Here I choose Pmin (frequency count = 1) as control value, and get negative values of free energies;<SPAN style="mso-spacerun: yes"> </SPAN><o:p></o:p></FONT></SPAN></P>
<P class="MsoNormal" style="MARGIN: 0in 0in 0pt; TEXT-INDENT: 14.25pt; LINE-HEIGHT: 150%"><SPAN style="FONT-FAMILY: SimSun"><FONT size="3">7. Convert the values in above three columns into a new matrix by using the method of XYZ Gridding. <o:p></o:p></FONT></SPAN></P>
<P class="MsoNormal" style="MARGIN: 0in 0in 0pt; TEXT-INDENT: 14.25pt; LINE-HEIGHT: 150%"><SPAN style="FONT-FAMILY: SimSun"><FONT size="3">8. According to the above new matrix, plot the final free energy landscape.<SPAN style="mso-spacerun: yes"> </SPAN><SPAN style="mso-spacerun: yes"> </SPAN></FONT><o:p></o:p></SPAN></P>
<P class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: 12.5pt"> <o:p></o:p></P></DIV>
<DIV><BR>--<BR>
<DIV><FONT face="Arial" color="#000000" size="2">Dx Li</FONT></DIV>
<DIV><FONT face="Arial" color="#000000" size="2">---------------------------------------</FONT></DIV>
<DIV><FONT face="Arial" color="#000000" size="2">Mechanic Engineering Department</FONT></DIV>
<DIV><FONT face="Arial" color="#000000" size="2">College of Engineering and Computing</FONT></DIV>
<DIV><FONT face="Arial" color="#000000" size="2">University of South Carolina</FONT></DIV>
<DIV><FONT face="Arial" color="#000000" size="2">300, Main Street, 29208</FONT></DIV>
<DIV><FONT face="Arial" color="#000000" size="2">Columbia, SC</FONT></DIV>
<DIV><FONT face="Arial" color="#000000" size="2">Tel: 803-9316307(M); 803-7771299(O)</FONT></DIV>
<DIV><FONT face="Arial" color="#000000" size="2">E-mail:Daixi@cec.sc.edu</FONT></DIV></DIV><br><br><span title="neteasefooter"/><hr/>
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