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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Received on Mon Sep 02 2013 - 14:00:02 PDT
