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 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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Received on Tue Sep 03 2013 - 05:30:03 PDT
