Dear Researchers,
I am trying to simulate a protein that binds a complex ligand. Small equilibration step was ok but failed while trying to heat the system due to high values of vander waals terms. When I went through discussion forums of AMBER and googling, one of reasons may be atomic clashes. When I checked the structure with AMBERTOOLS, the following warning were seen:
Warning: Atoms 3759:LYS_227@HE3 and 3827:ILE_232@HA are close (0.33)
Warning: Atoms 3761:LYS_227@HZ1 and 3830:ILE_232@CG2 are close (0.54)
Now, I am seeking to help in fixing bad structure of the proteins. I tried with variables steps of minimization, but still no luck.
Thank you for help,
Mahendra Thapa
yes, you need to verify the LYS 227 and LYS 232 because you have a hard clash, distance between two atom is less than Van der Walls radii, it's why you have a to large van der walls term of energy, it's that the alarm message said.
just move this two lysine in goor orientation and your problem will probably disappear
Just one short add: Lysine side chains are long and "flexible" (many are not "seen" in the electron density in the case of structures determined by X-ray crystallography). You should select one of the conformers though, since there are preferred conformations of the side chains. The program Coot has the possibility of going from one conformer to the next, and then to select the one that makes more sense (we crystallographers have electron density to guide us).
Hi
What are the steps you are doing from start? For minimization use steepest decent option.
Dear All
Thank you for helpful suggestions. To get the initial structure for the simulation, when I added hydrogen atoms in the structure and then minimized using Chimera, the problem got solved.
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