this sounds like a periodic imagine issue and not real dissociation. look
in the ptraj manual for the "image" command. there are also many examples
in the email archive- check the amber web site.
On Mon, May 7, 2012 at 6:38 AM, Emilio Lence <guitarro.de.meixente.gmail.com
> wrote:
> 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 - 04:30:03 PDT
