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<DIV dir=ltr><FONT face=Arial color=#000000 size=2>You could try</FONT></DIV>
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<DIV dir=ltr><FONT face=Arial size=2>trjconv -f -s -pbc res -ur compact -center -o</FONT></DIV>
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<DIV dir=ltr><FONT face=Arial size=2>Good luck.</FONT></DIV></DIV>
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<FONT face=Tahoma size=2><B>Von:</B> gmx-users-bounces@gromacs.org im Auftrag von ana johari<BR><B>Gesendet:</B> Mi 27.04.2011 08:55<BR><B>An:</B> gmx-users@gromacs.org<BR><B>Betreff:</B> [gmx-users] Fw: trjconv -pbc and broken reside<BR></FONT><BR></DIV>
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<DIV style="FONT-SIZE: 12pt; COLOR: black; FONT-FAMILY: 'times new roman', 'new york', times, serif"><SPAN class=Apple-style-span style="FONT-FAMILY: times, serif">dear justin,</SPAN></DIV>
<DIV style="FONT-SIZE: 12pt; COLOR: black; FONT-FAMILY: 'times new roman', 'new york', times, serif"><SPAN class=Apple-style-span style="FONT-FAMILY: times, serif">Hello,</SPAN><SPAN class=Apple-style-span style="FONT-SIZE: medium; FONT-FAMILY: 'Times New Roman'"><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-SIZE: medium; FONT-FAMILY: 'Times New Roman'"><FONT class=Apple-style-span style="FONT-SIZE: 12pt; COLOR: rgb(0,0,0); FONT-FAMILY: times, serif" face="'times new roman', 'new york', times, serif">separation</FONT></SPAN><SPAN class=Apple-style-span style="FONT-SIZE: medium; FONT-FAMILY: 'Times New Roman'"><FONT class=Apple-style-span style="FONT-SIZE: 12pt; COLOR: rgb(0,0,0); FONT-FAMILY: times, serif" 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="FONT-SIZE: 12pt; COLOR: rgb(0,0,0); FONT-FAMILY: times, serif"><FONT class=Apple-style-span face="'times new roman', 'new york', times,
serif">any advice was appreciate.</FONT></DIV>
<DIV style="FONT-SIZE: 12pt; COLOR: rgb(0,0,0); FONT-FAMILY: times, serif"><FONT class=Apple-style-span face="'times new roman', 'new york', times, serif">tanks,</FONT></DIV>
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