[gmx-users] Topology generated of a dimer protein

Shima Arasteh shima_arasteh2001 at yahoo.com
Sun Sep 9 14:42:20 CEST 2012

Hi all,

I am simulating a system of protein and water. My protein is composed of 2 monomers, each monomer has its own C- and N-terminus, so there are 2 N-terminals and 2 C-terminals.
I have a pdb of two monomers as dimer.pdb. 

I tried to generate topology of dimer.pdb. But 2 monomers are identified as one fragment which has one -N-terminus and one C-terminus! So the generated topology file and the total charge would be incorrect.
How can I solve it? Any suggestions please?

Your suggestions would be appreciated.

Thanks in advance.


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