I'm preparing a PDB to run a MD simulation in AMBER. I have noticed that some of the amino acid residues exist in double confirmation. Should I remove all the double confirmation before the minimization or would it take one by default? If I have to delete one between the two, which one should I remove? or would it be random as later I'm going through minimization. Please help.
Thank you in advance.
Thanks a lot Stéphane. You have perfectly understood my question. In case of NMR structure I also perform the same thing as you described, but because it is the same protein conformation I was hesitating about the fact, if I would delete the residue with higher occupancy.
Hi,
as already suggested, you have to decide for one conformation; otherwise you would not be able to create a valid topology file via leap.
So, have a look at the two conformations using a molecular viewer, and then chose one.
Regards
As Anselm said, you can visualizate all the RNM models in VMD. You load your .pdb file, and then you go to Graphical Representation- Trajectory- Draw Multiple frame, and put 0:total number of frames. If you prefer one more than another, you can save it, go to File (choosing first the protein in the Main box), then Save Coordinates, and you can choose the frame that you want to save.
Regards
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