<div>Dear Karunakaran,</div> <div> </div> <div>I don't think there is any error here.</div> <div> </div> <div>I have also made MD simulations of HIV-PR dimer with Gromacs, but I couldn't observed complete seperation of dimer to monomers. It seems after 1ns simulation, there is a seperation between tips of flaps. (I mean the seperation between Gly49, Ile50, Gly51 and Gly49', Ile50', Gly51').I measured about 5 Angstrom seperation (average), distance between the alpha carbon atoms for these residues after simulation. </div> <div> </div> <div>When you put some inhibitors to this cavity, this seperation may restricted.</div> <div> </div> <div>You may check the article: Schuster et al, Biochemistry, 42, 1326, 2003.</div> <div> </div> <div> </div> <div>Serdar Durdagi</div> <div> </div> <div> </div> <div> </div> <div><BR><BR><B><I>chandran karunakaran <ckaru2000@yahoo.com></I></B> schrieb:</div>
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Dear GMX users,<BR><BR>On running the MD for HIV protease as dimer<BR>structure, it gets separated after the energy<BR>minimization. (That’s dimer is separated into two<BR>monomers). <BR><BR>Could you kindly help me out in running HIV<BR>protease as dimer? <BR><BR>with thanks<BR>c.karunakaran<BR><BR><BR>*******************************+ <BR>Dr.Karunakaran Chandran +<BR>Biophysics Department + <BR>Medical College of Wisconsin +<BR>Milwaukee, WI-53226 +<BR>Resi.: 414-443-0085 +<BR>Off : 414-456-4034 +<BR>********************************<BR><BR><BR><BR>____________________________________________________________________________________<BR>Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase.<BR>http://farechase.yahoo.com/<BR>_______________________________________________<BR>gmx-users mailing list
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