<div><FONT size=3><SPAN style="FONT-FAMILY: Arial">Hi</SPAN><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"><?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></FONT></div> <div><FONT size=3><SPAN style="FONT-FAMILY: Arial">I want to perform peptide + popc membrane simulation. I download popc128a.pdb from</SPAN><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"><o:p></o:p></SPAN></FONT></div> <div class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=3><SPAN style="FONT-FAMILY: Arial">(</SPAN><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"><A href="http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies"><SPAN style="FONT-SIZE: 12pt">http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies</SPAN></A></SPAN><SPAN style="FONT-FAMILY: Arial">).</SPAN><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"><o:p></o:p></SPAN></FONT></div> <div><FONT size=3><FONT face="Times New
Roman">Before I introduce the peptide into the membrane, the water layer had to be broadened to ensure full solvation of the peptide .I increase the water layer using the following commands<o:p></o:p></FONT></FONT></div> <div><FONT size=3><FONT face="Times New Roman">1. editconf -f popc128a.pdb -o po_box.pdb -box 6.1065 6.1059 9.0000 -c<o:p></o:p></FONT></FONT></div> <div><FONT size=3><FONT face="Times New Roman">2. genbox -cp po_box.pdb -cs -o po_sol.pdb -p lip.top<o:p></o:p></FONT></FONT></div> <div><FONT size=3><FONT face="Times New Roman"> <o:p></o:p></FONT></FONT></div> <div><FONT size=3><FONT face="Times New Roman">Now, the no. of water molecules over the bilayer <SPAN style="mso-spacerun: yes"> </SPAN>increased . But, the problem is that there are water molecules inside the bilayer, which were absent incase of popc128a.pdb. How can I remove these
offending water molecules?<o:p></o:p></FONT></FONT></div><p>
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