[gmx-users] umberlla sampling of protein ligand complex

Negar Parvizi negar.parvizi at yahoo.com
Sun May 26 13:19:53 CEST 2019

Dear all,
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 ).

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GROMACS Tutorial
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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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