Dear all,
I have tried to simulate my protein-ligand system in water as usual, but my
protein has two Zn atoms that
bind 3Cys and 1 His (Zn1) and 4Cys (Zn2). I have browsed the literature and the
ML: the most common
suggestion that I had found was the usage of distance restraints in my protein
topology file.
After a bit of manual reading, I have set up my table for distance restraints
as follows:
[distance restraints]
620 98 1 0 1 0.18 0.30 0.35 1 ;Zn1 - His
620 120 1 0 1 0.18 0.30 0.35 1 ;Zn1 - Cys1
620 278 1 0 1 0.18 0.30 0.35 1 ;Zn1 - Cys2
620 304 1 0 1 0.18 0.30 0.35 1 ;Zn1 - Cys3
621 479 1 1 1 0.18 0.30 0.35 1 ;Zn2 - Cys4
621 222 1 1 1 0.18 0.30 0.35 1 ;Zn2 - Cys5
621 200 1 1 1 0.18 0.30 0.35 1 ;Zn2 - Cys6
621 455 1 1 1 0.18 0.30 0.35 1 ;Zn2 - Cys7
and the options used in the mdp file were:
disre = simple
disre_fc = 4000
disre_weighting = equal
I have noticed that, with respect to the first simulation that I had set up without distance restraints
(just a mistake) I do not see my two Zn atoms floating in solution like counterions or water molecules.
Neverthless, I am not really happy of the result I got: indeed, the second Zn atom (indexd with 1) is
more or less stable in its coordination pocket (Zn-S distance ~4-5 A), whereas the first Zn atom
(indexed with 0) is really strongly bound to Nd1 but it is not in the right coordination, being the
distance between Zn and Cys S atoms ~ 7-8 Angstrom.
Do you have any suggestion about how to get an improvement in my simulations ? Moreover, do you think
that the distance restraints table is badly written and/or does it contain errors ? My desire is to use a
distance restraints table that allows distance (without penalty) between 1.8 A and 3.5 A, which are the
same restraints tha have been used for structure determination by NMR (using CYANA).
Thanx a lot for any help
All the best
Luca
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