[AMBER] best Generalized Born solvation model for intrinsically disordered peptides

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Mon, 2 Sep 2013 23:48:12 +0300

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 :


, 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.


MD Implicit Solvent, infinite cut off


 nstlim=50000000, ! Number of MD-steps to be performed.
 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).

 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

! ntp=0, ! do not use pressure coupling

 ntc=2, ! bonds involving hydrogen are constrained with SHAKE
 tol=1.0e-8, ! Relative geometrical tolerance for coordinate resetting
in shake

 ntf=2, ! ommit force evaluations for bond interactions involving
 cut=999, ! Cut-off for vdW and electrostatic interactions.


 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
        ! of the LJ potential.

Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens
email: tevang.pharm.uoa.gr
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Mon Sep 02 2013 - 14:00:02 PDT
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