I generated files for minimization in Gromacs through Charmm-gui. But, when I was searching the bonds between Mg and amino acid in the section [bond], there were not. On the other hand, I could find possible interactions in the section [pairtype].
I would like to know if I could change the function from 1 to 6 in the section [pairtype] for harmonic restraints, because this change would not be possible according to the manual.
https://manual.gromacs.org/documentation/2019/reference-manual/topologies/molecule-definition.html
I attached my topology file
Dear Maria Solis
What do you want to do precisely? Keep the Mg atom at a given distance from the amino acid atoms?
Hello Nicola Piasentin !
Excuse me ..
I was looking to fix the magnesium since when I observe the trajectories of the molecular dynamics it moves in a noisy way. In addition, that rapid movement of magnesium happens from frame 300. I am concerned that this boisterous movement could alter the dynamics. In the reference, it does not mention that magnesium is linked with any amino acid.
Dear Maria Solis
What do you mean noisy way? To me it seems that it is diffusing around (supposing the volume is filled with water) like the other small molecule that is moving. Maybe you can calculate its diffusion coefficient and see if it is reasonable, but I don't understand why it should stay at a fixed location.
If you want to apply some kind of restraint to keep the ion at a given position then you must work in the .mdp file, and add lines to specify there what you want to do exactly (https://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html#com-pulling). If you modify the interactions in the .itp file of the force field you are modifying it for all those atom types in your system.
But as you said, if you prepared your system in CHARMM-GUI and the magnesium is not related to your particular set up, then it was added just to keep the total net charge zero, therefore why would you want to act on its dynamics?
Nicola Piasentin Reviewing the literature, the drug interacts with the protein through water molecules to stop the DNA cleavage process. Although I am not using DNA, I expected the drug to remain fixed in the center of the protein thanks to van der Waals interactions with surrounding water molecules.
In the preparation of the system I removed all the water molecules from the crystal, but I did the protonation of both the protein-Magnesion and the drug.
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