Thanks Bill. Indeed my protocol is essentially based on that tutorial only. I once again
tried to create the system from scratch several (6) times and ran all the steps. Analysis (energy,
temp, pressure, density and volume) of every run seems to be fine. But eventually I end
up with the same problem (voids in the solvent layers).
Can anyone share the protocol and the input files of successful protein-ligand solvent equilibration runs?
Thanks,
Senthil Natesan
> I am equilibrating the solvent (in solvated protein-ligand complex)
> using the following parameters.
> But at the end of heating phase itself (first 20 ps), after reimaging,
> I found that the solvent molecules forming many hollow spaces on the
> surfaces. MD runs seem to be stable and fine (temp, energy, density,
> please see the attached .out file).
Your heating phase (step 3) is constant volume. The next phase is constant
pressure (ntb=2) and thus should fix the vdw voids. E.g.
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/section5.htm
for a discussion of vdw voids.
Bill
> **********
> step 1
> **********
> complex: initial minimization - solvent and ions
> &cntrl
> imin = 1,
> ntpr = 500,
> maxcyc = 10000,
> ncyc = 5000,
> ntb = 1,
> ntr = 1,
> cut = 12.0
> drms = 0.001
> /
> Hold the protein fixed
> 500.0
> RES 1 285
> END
> END
> ************
> step 2
> ***********
> bztcomplex: initial minimization -entire system
> &cntrl
> imin = 1,
> ntpr = 500,
> maxcyc = 5000,
> ncyc = 1000,
> ntb = 1,
> cut = 8.0
> drms = 0.001
> /
> *********
> step 3
> ***********
> complex: heating phase MD - solvent and ions
> &cntrl
> imin = 0,
> ntpr = 100,ntwx = 100, ntwr = 1000,
> nstlim = 20000,dt = 0.001,
> tempi = 0.0, temp0 = 300.0,
> ntb = 1,
> ntr = 1,
> cut = 10.0
> ntt = 3, gamma_ln = 1.0
> /
> Hold the protein fixed
> 10.0
> RES 1 285
> END
> END
> *********
> step 4
> *********
> bztcomplex: equilibration phase MD - solvent and ions
> &cntrl
> imin = 0,irest=1, ntx=7,
> ntb=2, pres0=1.0, ntp=1,
> taup=2.0,
> ntpr = 100,ntwx = 100, ntwr = 1000,
> nstlim = 20000,dt = 0.001,
> tempi =300.0, temp0 = 300.0,
> ntr = 1,
> cut = 10.0
> ntt = 3, gamma_ln = 1.0
> /
> Hold the protein fixed
> 10.0
> RES 1 285
> END
> END
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Received on Mon May 17 2010 - 07:00:07 PDT
