[gmx-users] umberlla sampling of protein ligand complex
negar.parvizi at yahoo.com
Tue May 28 12:35:01 CEST 2019
I have a protein_Ligand complex which I want do Umbrella Sampling on it to find out free energy.for this purpose I used Justin tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ).
Here is my questiones:in tutorial he said:
Acetylated at the N-terminus of each chain of wild-type Aβ protofibril and after pdb2gmx command; he said choose:
"None" for the N-termini, and "COO-" for the C-termini1 - why he said COO-" for the C-termini?2- I don't know how should I do for my own Protein_Ligand complex? what points should be paied attention to find out where adding acetyl, COO or NH2?
I would appreciate any help
Tanks in advance,
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