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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>
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Received on Tue Sep 03 2013 - 05:00:04 PDT
