I want to calculate electrostatic interactions and van der waals interaction by using xyz coordinates from pdb file of DNA.
Is there any formula to calculate using xyz coordinates?
In the below given coordinates i want to calculate nonbonded interactions between 2 atoms like C and O(i.e 1 st and 2nd) using their XYZ coordinates?
HETATM 1 C ACE A 1 21.964 4.763 -5.072 1.00 0.00 C HETATM 2 O ACE A 1 22.957 4.500 -4.391 1.00 0.00 O HETATM 3 CH3 ACE A 1 22.152 5.500 -6.388 1.00 0.00 C HETATM 4 H1 ACE A 1 21.995 4.805 -7.211 1.00 0.00 H HETATM 5 H2 ACE A 1 23.164 5.897 -6.442 1.00 0.00 H HETATM 6 H3 ACE A 1 21.439 6.321 -6.460 1.00 0.00 H HETATM 7 C8' GPN A 2 18.417 1.449 -5.486 1.00 0.00 C HETATM 8 C7' GPN A 2 17.441 2.329 -6.302 1.00 0.00 C HETATM 9 O7' GPN A 2 16.277 1.956 -6.496 1.00 0.00 O HETATM 10 C5' GPN A 2 17.034 4.315 -7.713 1.00 0.00 C HETATM 11 C' GPN A 2 16.073 5.294 -7.025 1.00 0.00 C HETATM 12 O1' GPN A 2 15.333 5.995 -7.724 1.00 0.00 O HETATM 13 N4' GPN A 2 17.882 3.507 -6.805 1.00 0.00 N HETATM 14 C3' GPN A 2 19.265 3.951 -6.648 1.00 0.00 C HETATM 15 C2' GPN A 2 19.432 4.703 -5.323 1.00 0.00 C
One way to go about is using an MD program like GROMACS. You need to choose a forcefield and better run small energy minimization. After which you can extract these energies.
There is a tool called PLIP (Protein-Ligand Interaction Profiller), and i think it might be useful in your case.
The "pair interaction calculations" in NAMD software could calculate the interaction energy of two pair (or two group atoms) atom.
I have a dimer complex with unusual Metal to aqua bond length and which is why i am really confused whether there is actually a bond that exist...So, can you please provide me a way to find out some chemistry about it.
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