When i calculated the van der Waals' interaction energy between protein atoms and ligand atoms, i got energy values in +ve .
Example: atom1 distance atom2
C 1.82Å O
i got energy value: 600.598627344126.
pls help me and tell why it come like this? I taken formula from following references paper:
1) http://caps.ncbs.res.in/coilcheck/METHODOLOGY.html
2) http://homepage.univie.ac.at/mario.barbatti/papers/method/amber_1995.pdf
3) http://www.ncbi.nlm.nih.gov/pubmed/27400687
How much energy you are expecting ? you can calculate it manually.
other interactions are involved or not in the energy value you are reporting here?
Generally, energy values represented by -ve values. so i am expecting -ve values. no .. other interactions are not involved
if it is the only interaction considered, then +ve energy means your atoms are closer than the distance allowed in energy minimized state. You can calculate the energy of interaction manually.. this will confirm you are not making any obvious mistake in the input files.
May be closer distance between atoms is a problem. so how can i solve the problem? Is there any server for calculating VDW energy ??
well it might seem complicated but you can manually calculate vander waal energy by energy function used in molecular dynamics... use the formula attached with answer... you can get value of constant A and C from parameter file of some force field. A and C depends upon the interacting atoms...
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