[gmx-users] Prodrg question.

[Michal Kolinski]

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