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<DIV style="RIGHT: auto" dir=ltr><SPAN style="LINE-HEIGHT: 115%; FONT-FAMILY: 'serif'; FONT-SIZE: 14pt"><VAR id=yui-ie-cursor></VAR>Dear Users, </SPAN></DIV>
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<DIV style="TEXT-ALIGN: justify; MARGIN: 0in 0in 10pt" class=yiv2146708980MsoNormal><SPAN style="LINE-HEIGHT: 115%; FONT-FAMILY: 'serif'; FONT-SIZE: 14pt">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> </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:</SPAN></DIV>
<DIV style="TEXT-ALIGN: justify; MARGIN: 0in 0in 10pt" class=yiv2146708980MsoNormal><I><SPAN style="LINE-HEIGHT: 115%; FONT-FAMILY: 'serif'; FONT-SIZE: 14pt">g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx<B></B></SPAN></I></DIV>
<DIV style="TEXT-ALIGN: justify; MARGIN: 0in 0in 10pt" class=yiv2146708980MsoNormal><SPAN style="LINE-HEIGHT: 115%; FONT-FAMILY: 'serif'; FONT-SIZE: 14pt">Does it show me how the ligand affects the active site residues bond angles?</SPAN></DIV>
<DIV style="TEXT-ALIGN: justify; MARGIN: 0in 0in 10pt" class=yiv2146708980MsoNormal><SPAN style="LINE-HEIGHT: 115%; FONT-FAMILY: 'serif'; FONT-SIZE: 14pt">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" class=yiv2146708980MsoNormal><SPAN style="LINE-HEIGHT: 115%; FONT-FAMILY: 'serif'; FONT-SIZE: 14pt"><VAR id=yiv2146708980yui-ie-cursor></VAR>Sogol</SPAN></DIV>
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