Hello Hai,
Thanks for your comments. Now the conversation is getting interesting.
I used gbsa=0 with all GB models. I guess that is the less compact it could
get. At the end of the email is a complete list of parameter values I used.
I didn't do just that simulation. I have done several long aMD simulations
with igb 8
along with AMBER12SB or AMBER99SB-NMR1-ILDN of larger ID proteins or
smaller peptide fragments of them, but all ended up to helical forms. In
contrast, in TIP4P-Ew + AMBER99SB-NMR1-ILDN aMD runs these
proteins/peptides remain mostly disordered.
I'd be curious to know if there is any other parameter I could tweak to get
better results.
best,
Thomas
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 100, ntrx = 1, ntwr =
10000
iwrap = 0, ntwx = 1000, ntwv = 0, ntwe
= 0
ioutfm = 1, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 2, ntb = 0, igb = 8, nsnb
= 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
saltcon = 0.15000, offset = 0.19514, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000
alpb = 0
gbalphaH = 0.78844, gbbetaH = 0.79870, gbgammaH = 0.43733
gbalphaC = 0.73376, gbbetaC = 0.50638, gbgammaC = 0.20584
gbalphaN = 0.50336, gbbetaN = 0.31683, gbgammaN = 0.19292
gbalphaOS = 0.86781, gbbetaOS = 0.87664, gbgammaOS = 0.38788
gbalphaP = 1.00000, gbbetaP = 0.80000, gbgammaP = 4.85000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 10000000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Langevin dynamics temperature regulation:
ig = 934379
temp0 = 310.00000, tempi = 100.00000, gamma_ln= 5.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00000
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 100
On 3 September 2013 22:49, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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/
> >> _______________________________________________
> >> 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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Received on Tue Sep 03 2013 - 14:00:02 PDT
