[gmx-users] Joining peptide chains using Gromacs

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 23 06:13:21 CEST 2007

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? 

When starting a new thread, please delete the text of the email you 
replied to, so that you don't send pointless volume all around the 
internet and text searches stay more meaningful.

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.


More information about the gromacs.org_gmx-users mailing list