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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