In addition, are you using gbsa = 1 or 0? with nonpolar term added, you can
have more compacted structures.
On Tue, Sep 3, 2013 at 3:48 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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/
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>>
>> ======================================================================
>>
>> 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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>>
>
>
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Received on Tue Sep 03 2013 - 13:00:03 PDT
