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On 4/27/2011 4:55 PM, ana johari wrote:
<blockquote cite="mid:175323.95084.qm@web31602.mail.mud.yahoo.com"
type="cite">
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<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;"><span
class="Apple-style-span" style="font-family: times,serif;">dear
justin,</span></div>
<div style="color: black; font-family: 'times new roman','new
york',times,serif; font-size: 12pt;"><span
class="Apple-style-span" style="font-family: times,serif;">Hello,</span><span
class="Apple-style-span" style="font-family: 'Times New
Roman'; font-size: medium;"><font class="Apple-style-span"
face="'times new roman', 'new york', times, serif"
size="3"><font class="Apple-style-span" face="times,
serif" size="3">after 5ns MD,based on your </font>recommend,
I use"<font class="Apple-style-span" face="times, serif"
size="3"> trjconv -f -s -pbc -mol -center -o *.pdb"
command to get the whole protein without any </font></font></span><span
class="Apple-style-span" style="font-family: 'Times New
Roman'; font-size: medium;"><font class="Apple-style-span"
style="color: rgb(0, 0, 0); font-family: times,serif;
font-size: 12pt;" face="'times new roman', 'new york',
times, serif">separation</font></span><span
class="Apple-style-span" style="font-family: 'Times New
Roman'; font-size: medium;"><font class="Apple-style-span"
style="color: rgb(0, 0, 0); font-family: times,serif;
font-size: 12pt;" face="'times new roman', 'new york',
times, serif" size="3">,but I found some part of the
residue was broken,and some new bond at the end of some
residue was formed.I need the intact molecule for
docking,but how should I solve this problem.</font></span></div>
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<div style="color: rgb(0, 0, 0); font-family: times,serif;
font-size: 12pt;"><font class="Apple-style-span"
face="'times new roman', 'new york', times, serif">any
advice was appreciate.</font></div>
<div style="color: rgb(0, 0, 0); font-family: times,serif;
font-size: 12pt;"><font class="Apple-style-span"
face="'times new roman', 'new york', times, serif">tanks,</font></div>
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<br>
See <a href="http://www.gromacs.org/Documentation/FAQs">http://www.gromacs.org/Documentation/FAQs</a>
#9 and #11.<br>
<br>
Mark<br>
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