[gmx-users] Output of rotation

[Shima Arasteh]

Dear gmx users,

I have .pdb file. This .pdb file represents a dimer protein. When I try to generate a topology file of it, GROMACS asks for terminals one by one, ( 2 N-terminals, 2 C-terminals ) . But after rotation of protein, 2 terminals are lost and the total charge is incorrect.
The pdb file was visualized and its format seems to be correct.
Anybody knows what is the problem? How can I overcome this problem? 
Please help me

Thanks in advance.


Sincerely,
Shima