<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div style="TEXT-ALIGN: justify; MARGIN: 0in 0in 10pt" class=MsoNormal><SPAN style="LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 14pt; mso-ascii-theme-font: major-bidi; mso-hansi-theme-font: major-bidi; mso-bidi-theme-font: major-bidi">Dear Users, <?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></div>
<div style="TEXT-ALIGN: justify; MARGIN: 0in 0in 10pt" class=MsoNormal><SPAN style="LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 14pt; mso-ascii-theme-font: major-bidi; mso-hansi-theme-font: major-bidi; mso-bidi-theme-font: major-bidi">I am trying to analyze a ligand-protein simulation results. I read in the manual that using g_rms command with –bm option produces a matrix of average bond angle deviations. And only bonds between atoms in the comparison groups are considered. <SPAN style="mso-spacerun: yes"> </SPAN>Does it mean that it is for the bonds and their angles that are already in existence? (Not the ones that may be formed throughout simulation, I mean the ligand may for example interact with residues through H-bonds) .I have made a group in my index file named Active site (including only the active site residues), and I have a LIG group as well. If I choose these two groups for g_rms with this
command:<o:p></o:p></SPAN></div>
<div style="TEXT-ALIGN: justify; MARGIN: 0in 0in 10pt" class=MsoNormal><I><SPAN style="LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 14pt; mso-ascii-theme-font: major-bidi; mso-hansi-theme-font: major-bidi; mso-bidi-theme-font: major-bidi">g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx<B><o:p></o:p></B></SPAN></I></div>
<div style="TEXT-ALIGN: justify; MARGIN: 0in 0in 10pt" class=MsoNormal><SPAN style="LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 14pt; mso-ascii-theme-font: major-bidi; mso-hansi-theme-font: major-bidi; mso-bidi-theme-font: major-bidi">Does it show me how the ligand affects the active site residues bond angles?<o:p></o:p></SPAN></div>
<div style="TEXT-ALIGN: justify; MARGIN: 0in 0in 10pt; RIGHT: auto" class=MsoNormal><SPAN style="LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 14pt; mso-ascii-theme-font: major-bidi; mso-hansi-theme-font: major-bidi; mso-bidi-theme-font: major-bidi">And one more question, how can I study the ligand orientation in the active site?</SPAN></div>
<div style="TEXT-ALIGN: justify; MARGIN: 0in 0in 10pt; RIGHT: auto" class=MsoNormal><SPAN style="LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 14pt; mso-ascii-theme-font: major-bidi; mso-hansi-theme-font: major-bidi; mso-bidi-theme-font: major-bidi"><VAR id=yui-ie-cursor></VAR>Sogol<o:p style="RIGHT: auto"></o:p></SPAN></div>
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