[gmx-users] Interactions between tow chains of a protein

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 6 18:19:16 CET 2008

Polavarapu, Abhigna wrote:
>  Hi All,
>          I am abhigna. I wanted to simulate a protein which binds to
> Copper. Copper interacts with amino acids of Chain A and B of the
> Dimeric protein. When I convert the pdb file to topology file this is
> how it defines with A and B with protein and C and D with Copper. So I
> need to define a bond between Copper and amino acids in chain A and B.
> So How can I do that as I need to define the force field for copper in
> the .top file.

Probably the best way to do this is to define a new bond(s) in specbond.dat, 
which is in the share/top subdirectory of your Gromacs installation.  Then 
re-process your structure with pdb2gmx.


> [ molecules ]
> ; Compound        #mols
> Protein_A           1
> Protein_C           1
> Protein_B           1
> Protein_D           1
> SOL                20
> SOL                20
> Thank you
> abhigna_______________________________________________
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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