<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div>Dear All,<br><br>I have a lipid - peptide system and while running the production run I forgot to assign comm-grps, thus the peptide has actually shifted from the center towards one of the edges. I have searched the forum and tried all possible options in trjconv i.e. -center zero, -fit translation, progressive etc. but mostly the entire bilayer shifts but the peptide does not move from its place. I am selecting the "Protein" option from trjconv when it asks for "group used for centering"<br>How to translate the peptide only in a lipid-peptide system to a certain point? This is a short peptide in the top layer of the lipid bilayer and my bilayer center is at (0,0,0). I want to put the peptide at (0,0,1.7). I even tried using the shift option, but that does some weird things.<br>Searching
forum results in centering peptide in a water box i.e. peptide or protein at 0,0,0 and also mainly the threads that are already there talks about using trjconv center and translation options! I really apologize if I missed out any thread related to this and shall be really grateful if experts out there would kindly help me out.<br><br>eagerly waiting for the response,<br>Priyanka...<br></div></div><br>
<!--2--><hr size=1></hr> Unlimited freedom, unlimited storage. <a href="http://in.rd.yahoo.com/tagline_mail_2/*http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/">Get it now</a></body></html>