[modeller_usage] wrong topology for the ligand?

[Youbin Tu <>]

Hi all:

     I am using MODELLER7V7 to build a ligand-enzyme complex, I created 
the ligand and modified the library files. Everything worked well 
except the ligand in the final result seems too weird, for example the 
benzene is not planar and there are many bonds between 2 atoms which 
should only have one bond theoritically. 
     I thought maybe it is my problem when building the ligand. But 
when I tried to use GDP which  already existed in the library file. The 
final 
results still have the same problem. 
     Anyone knows how to deal with this kind of problem? Does it mean 
that we have to modify the par.lib or make restraints for bonds of the 
ligands? If so, can you tell me how to do that,any softwares are 
available for that purpose? 
      Your reply is highly appreciated. 

                                                                   
youbin