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<DIV><BR>I used prodrg server to generate topologies for some small
molecules. I’m a little bit confused about the bond length </DIV>
<DIV>that I’m getting (in structures after EM). <BR>For
example:<BR>1)<BR> c-c-c-c=c-c-c-c<BR>bonds are 1,53 ; 1,53
; 1,40 ; 1,40 ; 1,40 ; 1,53 ;
1,53<BR>2)<BR>c-c-c-c=c-c-c-c<BR>
| <BR>
C<BR>bonds are 1,53 ; 1,53 ; 1,53 ; 1,40 ; 1,40 ; 1,53 ;
1,53 and (for c-C) 1,53<BR>Is that because it is using atom type CR61 for
the = c - carbons?<BR>Is there a way to obtain
proper bond length? (can I just change <BR>[ bonds] entry in my topology for
atom pairs? <BR>Please give me some comment on this, thanks in
advance.<BR>Michal<BR></DIV></FONT></BODY></HTML>