I want to build a system of multiple, identical peptides, I saw other users suggest this documentation link http://www.gromacs.org/Documentation/How-tos/Multiple_Chains#Identical_chains
However, this link is not working, would someone recommend me simmilar documentation or provide some professional tip ?
Thanks in advance
Hi Amr Abbas,
You can use gmx insert molecule option to generate your initial topology of multiple chains of identical peptides. For the rest of the things, you can follow the Gromacs tutorial.
Hope this may help you!
Hi, simulating multiple peptides is the same as simulating a single peptide, you just need starting structure. Once, you got the starting structure, you can feed it to pdb2gmx and it will handle the rest.
The question is how you get multiple identical peptides. Either docking or manual assembly is your choice or depends on what you want to accomplish.
Good luck
do you want to simulate a peptide monomer to form a complex? or it's a protein-protein interaction that you want to simulate??
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