<br /><br /><span>On 01/31/11, <b class="name">bharat gupta </b> <bharat.85.monu@gmail.com> wrote:</span><blockquote cite="mid:AANLkTimthPPEmo-S6kXGnWEbrZ6CaBUmhG+TgD21XAEH@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,<div><br /></div><div>I am completed a 3 ns simulation of a 230 aa protein .. Now I want to check whether the water is entering the proteins and through which side of the protein .. Since the whole protein is surrounded by water I don't know how this can be done .. is there any command to check .. also I have tried doing it in VMD but there I am not able to do so ??</div></div></blockquote><br />Use g_select to create index groups of waters within a known distance of a central point. Then look at those groups in VMD.<br /><br />Mark<br /><blockquote cite="mid:AANLkTimthPPEmo-S6kXGnWEbrZ6CaBUmhG+TgD21XAEH@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"><div ><br/></div>
<div><br /></div><div>Pls help<br clear="all" /><br />-- <br />Bharat<br />Ph.D. Candidate<br />Room No. : 7202A, 2nd Floor<br />Biomolecular Engineering Laboratory<br />Division of Chemical Engineering and Polymer Science<br />Pusan National University<br />
Busan -609735<br />South Korea<br />Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>Mobile no. - 010-5818-3680<br />E-mail : <a href="mailto:monu46010@yahoo.com" target="1">monu46010@yahoo.com</a></div><br />
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