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