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<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT
face="Times New Roman"><SPAN lang=DE-LI
style="mso-ansi-language: DE-LI">Bond</SPAN><SPAN lang=DE-LI> </SPAN><SPAN
lang=EN-US>length</SPAN><SPAN lang=EN-US style="mso-ansi-language: PL">
</SPAN><SPAN style="mso-ansi-language: PL">– prodrg?<?xml:namespace prefix = o
ns = "urn:schemas-microsoft-com:office:office"
/><o:p></o:p></SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>I started to use prodrg to generate topologies for
my molecules.</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>Can someone please explain why did I obtain
different bond length</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>for set of similar molecules:</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes">
</SPAN><SPAN style="mso-spacerun: yes"> </SPAN>c=c-c<SPAN
style="mso-spacerun: yes"> </SPAN><SPAN
style="mso-spacerun: yes"> </SPAN>bond length <SPAN
style="mso-spacerun: yes"> </SPAN><SPAN
style="mso-spacerun: yes"> </SPAN>1.39<SPAN
style="mso-spacerun: yes"> </SPAN>;<SPAN style="mso-spacerun: yes">
</SPAN>1.53</FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman"><SPAN
style="mso-spacerun: yes"> </SPAN>c-c=c-c<SPAN
style="mso-spacerun: yes"> </SPAN><SPAN
style="mso-spacerun: yes"> </SPAN>bond length <SPAN
style="mso-spacerun: yes"> </SPAN><SPAN
style="mso-spacerun: yes"> </SPAN>1.53<SPAN
style="mso-spacerun: yes"> </SPAN>;<SPAN
style="mso-spacerun: yes"> </SPAN>1.39 ;
1.53</FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>c-c-c=c-c-c bond length 1.53 ; 1.39 ; 1.39 ; 139 ;
1.53 </FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><o:p><FONT
face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>Please give me some comment on this.
</FONT></SPAN></P></FONT></DIV></BODY></HTML>