Hello.
My system its a homotrimer, each subunit has 144 amino acids and a ligand,
with a binding site close to de interfaces between two subunits. I observed
that after equilibration at least one of the subunits appears on the
opposite side of the truncated octahedron of waters leaving the ligand
behind. I tried increasing the water box from 10 to 12 Armstongs, with the
same result. If I run the MD simulation, I observed that: sometimes the 3
subunits came together; other times each one of the 3 subunits is in one
corner of the box; but mostly I have two subunits close, near the the third
ligand, and the third protein chain in the opposite site. It looks like
boundary conditions were applied to the protein chain, because in the place
where the subunit should be, there is a "hole" in the water molecules
surface with a complementary shape to the "missing" subunit. But if I
measure distances using ptraj between the ligand an the corresponding
subunit, the values are normal, it's like the subunit was in the right
place and not far from the ligand. But pdb structures generated with ptraj
or ambpdb show the subunit far from the ligand. When using VMD to see the
trajectory, the same thing happen.
I also tried to delete 2 of the ligands, leaving only one, but after
equilibration I have the same problem. I donīt know if I'm doing something
wrong when generating the pdb using ptraj, or during equilibration time.
I'm using amber 10, ambertools 11. The equilibration input files are as
followed:
> eq1 temp = 300, k = 20
>> &cntrl
>> nstlim = 10000, dt = 0.002,
>> ntx = 7, irest = 1,
>> ntpr = 500, ntwr = 500, ntwx =500,
>> tempi = 300., temp0 = 300.,
>> ntt = 1,
>> ntb = 2, ntp = 1,
>> ntc = 2, ntf = 2,
>> ntr = 1,
>> restraint_wt = 50.0, restraintmask=':1-435'
>> &end
>>
> Restrains are reduces by 5 in each equilibration step, until reach 0.
The MD input:
#DINAMICANA
>> &cntrl
>> ntx = 7, irest = 1, ntrx = 1,
>> ntxo = 1, nmropt = 1,
>> ntpr = 1000, ntwx =1000,
>> ntf = 2, ntb = 2, dielc = 1.0,
>> cut = 9., nsnb = 10, scnb = 2.0, scee = 1.2,
>> imin = 0, ibelly = 0, iwrap = 1,
>> nstlim = 10000, dt = 0.002,
>> temp0 = 300.0, tempi = 300.0,
>> ntt = 1, vlimit = 20.0,
>> ntp = 1,
>> ntc = 2, tol = 0.00001, pres0=1, comp=44.6,
>> jfastw=0, nscm=1000,
>> &end
>> &wt type='END' &end
>> &ewald
>> skinnb=1, dsum_tol=0.000001,
>> &end
>>
>> Thanks in advance.
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Received on Mon May 07 2012 - 04:00:03 PDT
