<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">Dear Gromacs users,<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></FONT></DIV>
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<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">I am currently working on Dynamic simulation studies </FONT><FONT face="Courier New">using GROMACS software. </FONT><FONT face="Courier New">In my current work I want to do simulation of a protein containing Fe-S cluster</FONT><FONT face="Courier New">. If i directly do through pdb2gmx then it is giving a error massage like "FES in not included in .rtp file". Regarding this I went through the Article "Gromacs Tutorial </FONT><FONT face="Courier New">for Drug-Enzyme Complex" which has shown clearly step-by-step how to </FONT><FONT face="Courier New">include new topologies for drug/ligand molecules. </FONT><FONT face="Courier New">But I was not successful in running the dynamics. </FONT><FONT face="Courier New">The "Drug-Enzyme complex" tutorial was </FONT><FONT face="Courier New">specific for ligands/Drugs that do not form part of the protein chain. But </FONT><FONT
face="Courier New">if I want to include topology for Fe-S cluster </FONT><FONT face="Courier New">which occur within the protein chain, how to do it?<o:p></o:p></FONT></DIV>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New"><o:p></o:p></FONT> </DIV>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">I tried according to the tutorial but was unsuccessful all the time.<o:p></o:p></FONT></DIV>
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<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">I'll be very grateful if you can outline me the procedure to be<o:p></o:p></FONT></DIV>
<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">followed in such cases.<o:p></o:p></FONT></DIV>
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<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">Thank you,</FONT></DIV>
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<P class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">Amrita Paul</FONT></DIV>
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