problems running amber parm7

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Jan 19 2015 - 13:03:44 CST

Hello:

I am experiencing problems in running amber parm7/rst (parm10) in periodic
box tip3p solvation. I used the same settings that proved efficient in past
work with parm9 for a protein with a metallic center:

# Approximations for nonbonded interactions
cutoff 9 # for vdW and elctrostatic interactions
switching on
switchDist 6 # < cutoff
pairListDist 11 # between pair of atoms for vdW and electrost
outputpairlists 1000
margin 0

# Multistep integrator parameters
timestep 1.5 # 1.5 fs/step
nonbondedFreq 2 # nonbonded forces every two steps
stepspercycle 20 # redo pairlist every 20 steps
fullelectfrequency 2 # number of timesteps between electr evaluation

# PME settings
PME on
PMETolerance 1.0e-6
PMEInterpOrder 4 # i.e. cubic spline
PMEGridSizeX 147 # size of fftw grid on x dimension
PMEGridSizeY 115
PMEGridSizeZ 102
PMEGridSpacing 1.0

# periodic settings
# Don't set the periodic cell basis if you have also specified an .xsc
# cellBasisVector1 138.96 0. 0.
# cellBasisVector2 0. 105.38 0.
# cellBasisVector3 0. 0. 91.97
cellOrigin 71.08314514160156 54.25843811035156 47.91973114013672

# output
outputName ./min-05
outputEnergies 500 ;# multiple of fullElectFrequency or viceversa
restartfreq 100
binaryrestart yes
binaryoutput no
# wrapNearest no
# wrapAll on

seed 3971

# Minimize protocol (steps multiple of stepspercycle)
# minimization on # default off
minTinyStep 1.0e-6 # default 1.0e-6
minBabyStep 1.0e-2 # default 1.0e-2
minLineGoal 1.0e-4 # default 1.0e-4

velocityQuenching on # default off
maximumMove 1.5 # default 0.75 x cutoff/stepsPerCycle = 0.5

Minimization proved difficult so that I went to velocityQuenching. That
went on well from ts/VelQuen 0.01/0.01 to 1.5/1.5, the last for 1000 steps.
Continuing under the latter conditions caused notable denaturation of the
protein (loss of alpha helicitiy) while the water box, from cubic became
nearly spherical.

The enzyme comprises several chains and a transition-metal active center,
bound to the protein backbone through covalent carbon-carbon bonds. The
conformation of the active center is maintained well until min-05 as the
protein above, then it suffers somewhat from the protein degradration.

I wonder whether more appropriate settings could be used. I*t is important
to mention that no denaturation of the protein was observed under implicit
conditions (GBIS/SASA) even on heating to 300K.*

Thanks for advice
francesco pietra

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