[gmx-users] Joining peptide chains using Gromacs

[Mark Abraham]

Grace Mugumbate wrote:
> Dear Gromacs Users,
> 
> I am building a G-protein coupled receptor molecule. I have used homology modelling to build the seven helices and Molecular dynamics with Gromacs to build the loops. I then converted the .gro files to .pdb files using trjconv. Now I would like to join the loops to the helices, is there a way of doing that with Gromacs? 

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If you have a structure file of your whole protein, and you have an .rtp 
file for your force field that has all of your residues, then this is a 
straightforward job for pdb2gmx. Check out chapter five of the manual if 
you haven't already done so.

Mark