<br /><br /><span>On 01/27/11, <b class="name">bharat gupta </b> <bharat.85.monu@gmail.com> wrote:</span><blockquote cite="mid:AANLkTimCzHUKTu4kvt7iP41d+utwTtSPKZm1HwD7ZPdt@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">Hi,<br /> <br />I did a 3ns simulation of a 236 amino acid protein (GFP, a beta barrel protein), after checking the trajectory it seems that from the first frame itself almost half portion of the two beta strands (159-171, 174-187) of GFP got converted into a loop like structure .. which should not happen in general.. and this change is found to be present from the first frame itself... </div></blockquote><br />If it's in the first frame, when was it written and how does it compare to the coordinates you gave to grompp?<br /><br />Mark<br /><br /><blockquote cite="mid:AANLkTimCzHUKTu4kvt7iP41d+utwTtSPKZm1HwD7ZPdt@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">So I want to know where can the fault be ... I followed the instructions for simulation from the lysozyme tutorial.. Pls help ..<br clear="all" />
<br />-- <br />Bharat<br />Ph.D. Candidate<br />
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