In case of AGE amino acid of proteins get modified by the glycating agents such as sugar, glucose and other molecules. hence the normal amino acid was modified by some molecular fragment which is linked through covalent bond. In order to do the molecular dynamics for the modified structure how to find out the toplogy (atom charges) and parameter (force field such as bond, angle constant) files for those modified amino acids and how to integrate the topology and parameter files with gromacs force field to run the simulation.
1. Take the modified amino acid residue.
2. Cap the amino and carboxyl ends.
3. Obtain electrostatic potential for the model molecule using ab initio quantum mechanics at the level of theory compatible with the force field.
4. Fit the electrostatic potential as partial atomic charges.
5. Manually adjust the charges to account for the missing artificial caps in the original modified amino acid residue.
6. Assign atom types to the modified amino acid residue according to the force field.
7. Check if all bonds, bond angles, and dihedral angles are defined by the force field.
8. Add the missing bonds, bond angles, and dihedral angles (quick-n'-dirty: simply by analogy) to the force field library.
9. Feel exhausted (optional).
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Not a gromacs user.
Try Desmond for MD.. you can do it ..as it has inbuilt parameters for different atom types..
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