[gmx-users] How can I ...?

[mohsen ramezanpour]

Dear All
I want to generate .top and .gro files for protein-ligand complex.
there are many problems,can every body guide me?
Actually it is my M.sc thesis and it has taken much time of me.

problems:
1-after using PRODRG server the vector boxes for  are not the same
2-ligand's coordinates change very much,then my structure is not the
original one that I wanted(I think it is because of box vector)
3-there are a few atom types which is not familiar for grompp

Actually I don't know what I can do with this condition
If any of you can generate them for me please say me to send complex.pdb
file in his/her email.
Thanks in advance for your guidance
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