1-4 interactions

User discussions
1

Hello,

I have a system of a protein and a ligand. When building topology, I used pdb2gmx for the protein and
other tools for the ligand. I got a itp file for the ligand, then append it in the master topology files.

As Glycam force field (different scaling factor for 1-4 interactions) was used for the ligand, the parameters for 1-4 interactions of the ligand are explicitly included in the itp file, [pairs_nb].

Then when running simulations, how are the 1-4 interactions within the ligand being calculated, using the explicit parameters in the itp file, or grompp will generate new parameters based on the protein force field (different scaling factor)? Any comments are welcome and appreciated!

All the best,
Qinghua

2

Hi,
“Then when running simulations, how are the 1-4 interactions within the ligand being calculated, using the explicit parameters in the itp file, or grompp will generate new parameters based on the protein force field (different scaling factor)? Any comments are welcome and appreciated!”

The last parameters defined in the topology (in your case the one in the directive [pairs_nb] of “ligand”.itp file) will be used.

Just a comment [pairs_nb] is intended for free-energy simulations (see http://manual.gromacs.org/current/reference-manual/topologies/molecule-definition.html#pairinteractions). An alternative is [pairs].

Best regards
Alessandra

3

Hello Alessandra,

Thanks a lot for your confirmation on it!
I guess [pairs_nb] is equivalent to [pairs], if we know what we intend to do, right?

All the best,
Qinghua

4

Yes, knowing that you have to define 4 parameters
Best regards
Alessandra

5

Thanks a lot Alessandra!