normal Bonds between two chains/molecules

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3 years 9 months ago #8589 by amin_sagar
Bonds between two chains/molecules was created by amin_sagar
Dear All,
I am trying to simulate a protein-protein complex but it dissociates during the course of simulation. I would like to apply some restraints on the interface residues. When I use martinize.py, I get two separate itp files and it seems that the gromacs tool genestr needs the atoms to be part of the same molecule type.
Is there a way to add an elastic network between the interface residues of two different chains.
I would really appreciate any suggestions.

Best,
Amin.

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3 years 9 months ago #8592 by riccardo
Replied by riccardo on topic Bonds between two chains/molecules
I think the way to go is to obtain a unique itp out of the two proteins. I am not sure if this can be done by either:

1) first merging the pdbs and martinize will the produce a unique itp (hopefully then martinize takes care of the interface elastic network?) - not sure if this is what you already tried

2) running martinize on the two proteins pdb separetely, then merge by hand (i.e., with an ad-hoc script) the two itps. After merging, you would have to add by hand extra elastic bonds at the protein-protein interface. This is definitely possible, albeit a bit more time-consuming

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3 years 9 months ago #8593 by amin_sagar
Replied by amin_sagar on topic Bonds between two chains/molecules
Thanks for the answer. I have already tried the first part. That's how I originally built the system. It seems that when I start with the merged pdb, there is elastic network within the chains but not between the chains.
Then I ran martinize on the two proteins separately. This is what I actually need to do as I need the elastic network on only one of the proteins and the interface.
Does generating a merged itp involve just pasting one below the other and changing the atom numbers?

Best,
Amin.

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3 years 9 months ago #8594 by riccardo
Replied by riccardo on topic Bonds between two chains/molecules

Does generating a merged itp involve just pasting one below the other and changing the atom numbers?


Yes, exactly. The atom number shifting required for the protein which goes after is the one that requires automation (in order not to go insane).

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3 years 9 months ago #8595 by amin_sagar
Replied by amin_sagar on topic Bonds between two chains/molecules
Thanks. Seems like I should be able to do it.

Best,
Amin.

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