[gmx-users] Topology generated of a dimer protein

Justin Lemkul jalemkul at vt.edu
Sun Sep 9 14:44:39 CEST 2012

On 9/9/12 8:42 AM, Shima Arasteh wrote:
> 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?

The chains need to be either separated by a TER entry or have different chain 
identifiers.  pdb2gmx uses the -chainsep option to control the criteria for a 
new chain, and by default it uses either of these.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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