Hi Everyone!
I am trying to use an adapted bias MD, with DFTB/FF99SB coupled potential, but i can't map the full energy surface. The questionable reaction is a simple glutaminase enzyme reaction, where the nucleophile thiolate (cysteine sulfur) attack on the side-chain amidic carbonile carbon, while thiolate's ion pair (imidazolium ion, eg. double protonated histidine) donate its delta proton to the glutamine amidic nitrogen. I am using 0.5 fs time step for the dynamics (awesome slowly!!! XD ) and ntt=2 /ntf=2/qmshake=0 for shake, the ncsu_abmd and qmmm sections are below. The flooding time is changed from 0.005 ps to 100 ps, but the only chemical reaction is a proton transfer from imidazolium to thiolate, which is nice but in point of fact doesn't interesting. So I would like to ask that what would be the reason why doesn't happen anything that worth mentioninig ( Nu:- attack, and proton transfer, or anything...)? The energy surface has only two minima and they
belong to the thiolate and protonated thiolate and of course one saddle point between them, the other part of the surface is zero (unexplored?!). In the outputs the abmd (LCOD variables) and qm/mm section is correct and i tried PM3, PM6, AM1 semiempirical methods, the results are same. It is possible that the qm/mm can't compatible with the ncsu_abmd???
An other question is the resolution of LCOD. The manuals says it is the spatial resolution. What is its dimension? It isn't Angströms, because with 1.0 resolution and 7 Angström CV length, gives 29 point per CV, so it is 0.24 Angström (7/29). By the way I changed the resolution from 0.025 to 3.0, futilely.
Thank You in anticipation!
A. Fekete
Univ. Debrecen, HUngary
&qmmm
qmmask=':137,178,28', ! His, Cys, Gln
qmcharge=0,
qm_theory='DFTB',
dftb_3rd_order='PA'
qmshake=0,
writepdb=1,
/
ncsu_abmd
mode = FLOODING
monitor_file='abmd.txt'
monitor_freq=5
timescale=0.005 ! in ps
umbrella_file='umbrella.nc'
variable
type = LCOD
i = (2792, 2793, 2793, 443) ! His-ND --- His-HD --- His-HD --- Gln-NE
min = -3.5 max = 3.5
resolution = 1.0
r = (1.0, -1.0)
end variable
variable
type = LCOD
i = (2154, 441, 441, 443) ! Cys-SG --- Gln-CG --- Gln-CG --- Gln-NE
min = -3.5 max = 3.5
resolution = 1.0
r = (-1.0, 1.0)
end variable
end ncsu_abmd
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Received on Wed Sep 03 2014 - 02:00:02 PDT
