<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 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" face="'times new roman', 'new york', times, serif" style="color: rgb(0, 0, 0); font-family: times, serif; font-size: 12pt; ">separation</font></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" style="color: rgb(0, 0, 0); font-family: times, serif; font-size: 12pt; ">,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><div><div><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">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><div style="color: rgb(0, 0, 0); font-family: times, serif; font-size: 12pt; "></div>
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