On Tue, Sep 3, 2013 at 8:03 AM, Thomas Evangelidis <tevang3.gmail.com>wrote:
> AMBER12SB. As stated in the AmberTools13 manual (I may have read it
> elsewhere too) that's the only ff that can be used with igb 8.
I disagree with this information. Technically, you can use igb=8 with any
desired force field. Our work used wildly used ff99SB force field with
igb=8 and got nearly quantitative agreement between simulation and
experiment for our tested small protein (TC5B and HP5F). In the past,
people used a specific combination of force field and solvent model, like
ff96 + igb5, to seek for error cancellation. However, this kind of
cancellation should be avoided by using more accurate force field and
solvent model.
Anyway, how long is your simulation? In our test cases, we also have
quantitative agreement between gb8 and TIP3P data for unstructured Ala10
system or helical system like HP1 peptide. For a small system like yours, I
suggest to use REMD to perform extensive sampling since the structure might
stuck in local minimum in microsecond time scale in regular MD simulation.
You can do further by running explicit solvent simulation to compare.
For igb7, this model just doesn't "like" any folded structure, so you
should expect to get lots of unstructured conformation. However, this does
not mean it will give you the correct answer.
Hai Nguyen
> I also made
> sure to use mbondi3 with igb 8 and bondi with igb 7.
>
>
> On 3 September 2013 14:56, Carlos Simmerling <carlos.simmerling.gmail.com
> >wrote:
>
> > The physics of solvation should not differ for folded vs ID peptides. You
> > may see behavior with igb=7 that matches your expectations, because it
> > tends to give overly solvated, unstructured peptides even when they
> should
> > be folded.
> >
> > You don't mention the protein force field used, which is critically
> > important.
> > On Sep 2, 2013 4:50 PM, "Thomas Evangelidis" <tevang3.gmail.com> wrote:
> >
> > > Dear AMBER community,
> > >
> > > I want to assess qualitatively the interaction potential between an ID
> > > protein and ID peptides with implicit solvent (due to the excess speed
> > > gains on GPUs). I am using as a test case a 13mer peptide which has
> been
> > > studied with NMR and CD and was found to be unstructured. So far I have
> > > tested igb 8 and 7 and I have found 7 to be better. Although 8 is the
> > > latest and is rumoured to be the current standard choice :
> > >
> > > http://archive.ambermd.org/201210/0029.html
> > >
> > > , it folds the peptide to an alpha-helix after ~17 ns of unbiased MD
> > using
> > > the parameters quoted at the end of the message. In contrast, when
> using
> > > igb 7 the peptide has some helical propensity but is mostly
> unstructured
> > > (helical and random coil conformations are in equilibrium).
> > >
> > > Does anyone have experience with such kind of systems to suggest a GB
> > > solvation model? Is there any parameter I could tweak to get better
> > results
> > > with igb 8 or should I stick to igb 7 ?
> > >
> > > thank you in advance for any suggestion.
> > >
> > > ~Thomas
> > >
> > >
> > > MD Implicit Solvent, infinite cut off
> > >
> > > &cntrl
> > >
> > > ! MOLECULAR DYNAMICS
> > > nstlim=50000000, ! Number of MD-steps to be performed.
> > > dt=0.002,
> > > ntx=1, ! read coordinates and velocities from the restart file
> > > irest=0, ! this is not a simulation restart
> > > ntpr=100, ! print energy every 100 steps
> > > nrespa=1, ! evaluate forces every step
> > > ntwr=10000, ! write restart file (.restrt) every 5000 steps
> > > ntwx=1000, ! save coordinates every 5000
> > > ntb=0, ! no PBC with GB solvent
> > > igb=8, ! use the optimized GBn implicit solvent model (ibg=8)
> > > (better than simple GB [igb=1] or OBC[igb=2,5], although less tested)
> > > saltcon=0.15, ! salt concentration
> > > ioutfm=1, ! use binary NetCDF format for the coordinate and
> velocity
> > > trajectory files (mdcrd, mdvel and inptraj).
> > >
> > > ! TEMPERATURE CONTROL
> > > tempi =100.0, ! initial temperature
> > > temp0=310.0, ! reference temperature at which the system is to be
> > > kept, if ntt > 0
> > > ntt=3, ! Use Langevin thermostat.
> > > gamma_ln=5, ! Damping coefficient for Langevin dynamics in ps - 1.
> > > tautp=2.0, ! Time constant, in ps, for heat bath coupling for the
> > > system, if ntt = 1
> > > ig=-1, ! The seed for the pseudo-random number generator
> > >
> > > ! PRESSURE CONTROL
> > > ! ntp=0, ! do not use pressure coupling
> > >
> > > ! BOND CONSTRAINTS
> > > ntc=2, ! bonds involving hydrogen are constrained with SHAKE
> > > tol=1.0e-8, ! Relative geometrical tolerance for coordinate
> > resetting
> > > in shake
> > >
> > >
> > > ! ELECTROSTATICS & VDW
> > > ntf=2, ! ommit force evaluations for bond interactions
> involving
> > > H-atoms
> > > cut=999, ! Cut-off for vdW and electrostatic interactions.
> > >
> > > &end
> > >
> > > &ewald
> > > vdwmeth=1, ! Apply an analytical tail correction to the reported
> vdW
> > > energy and virial that is equal to the amount lost due to switching and
> > > cutoff
> > > ! of the LJ potential.
> > > &end
> > >
> > >
> > >
> > > --
> > >
> > > ======================================================================
> > >
> > > Thomas Evangelidis
> > >
> > > PhD student
> > > University of Athens
> > > Faculty of Pharmacy
> > > Department of Pharmaceutical Chemistry
> > > Panepistimioupoli-Zografou
> > > 157 71 Athens
> > > GREECE
> > >
> > > email: tevang.pharm.uoa.gr
> > >
> > > tevang3.gmail.com
> > >
> > >
> > > website: https://sites.google.com/site/thomasevangelidishomepage/
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> >
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Tue Sep 03 2013 - 13:00:03 PDT
