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 ).
| | | 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, Negar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
