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<DIV style="FONT-FAMILY: times new roman, new york, times, serif; FONT-SIZE: 12pt">Dear All,</DIV>
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<DIV style="FONT-FAMILY: times new roman, new york, times, serif; FONT-SIZE: 12pt" class=ms__id616>According to the lysozyme model in the tutorial of <STRONG style="RIGHT: auto">Justin Lemkul </STRONG>in <A href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html</A>, I am runing a 2 chain protein complex MD, and the steps are exactly same as in that on-line tutorial except that I use the 2 chain protein rather than laysozyme. In the preparation steps, GROMACS produces 2 *.itp file,ne for chain A, one for chain B. But in the following steps, I find the 2 *.itp files have never been used by the following command. Thus sometimes I am suspicious for the following steps whether the MD was done only on Chain A or on both Chains.</DIV>
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<DIV style="FONT-FAMILY: times new roman, new york, times, serif; FONT-SIZE: 12pt" class=ms__id616>Will you please clarify why GROMACS produces the 2 *.itp files but never used them in the following MD steps? Have I done something wrong on my 2 chain protein MD?<VAR id=yui-ie-cursor></VAR></DIV>
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<DIV style="FONT-FAMILY: times new roman, new york, times, serif; FONT-SIZE: 12pt" class=ms__id616>I am looking forward to getting your reply.</DIV>
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<DIV style="FONT-FAMILY: times new roman, new york, times, serif; FONT-SIZE: 12pt" class=ms__id616>Cheers,</DIV>
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<DIV style="FONT-FAMILY: times new roman, new york, times, serif; FONT-SIZE: 12pt" class=ms__id616>Acoot</DIV></DIV></div></body></html>