equilibrated the system

From: Xiaoqing Wang (kitty_wxq_at_yahoo.com.cn)
Date: Tue Jan 11 2005 - 08:43:17 CST

Hi all

I have downloaded an example of an equilibration (or “restrained”) run
input file(restrained_md_example.in) in web site
http://mccammon.ucsd.edu/~rlaw/ctbp_workshop_rlaw.htm .

#forcefield
paratypecharmm on
parameters par_all27_prot_lipid.inp
#molecules
structure ions_added.psf
coordinates ions_added.pdb
bincoordinates after_min.restart.coor
#binvelocities a.restart.vel
extendedSystem after_min.xsc
temperature 310
#reassignFreq 100
#reassignTemp 25
#reassignIncr 25
#reassignHold 300
#constraints
constraints on
consref protein_only.coor
conskfile protein_cons.pdb
conskcol X
#temp & pressure coupling
langevin on
langevinTemp 10
langevinDamping 1
#useGroupPressure yes
#useFlexibleCell no
#LangevinPiston on
#LangevinPistonTarget 1
#LangevinPistonPeriod 200
#LangevinPistonDecay 500
#LangevinPistonTemp 10
#output
outputname restr_md
outputEnergies 10
restartfreq 500
DCDfreq 500
binaryoutput no
binaryrestart yes
outputTiming 100
wrapAll on
wrapNearest on
#integrator
timestep 1
nonbondedFreq 1
fullElectFrequency 4
stepspercycle 20
#approximations
rigidBonds all
rigidTolerance 0.00000001
cutoff 12
switching on
switchdist 10
pairlistdist 14
margin 3
exclude scaled1-4
1-4scaling 1.0 # 1.0 for Charmm, 0.833333 for Amber
PME on
#cellBasisVector1 114.39 0 0
#cellBasisVector2 0 120.16 0
#cellBasisVector3 0 0 141.96
PMEGridSizeX 120
PMEGridSizeY 120
PMEGridSizeZ 120
#minimize 1000
run 250000

My question is how to prepare consref and conskfile files if I want to
restrain protein?

Thanks!!!

-- 
Wuhan University
Wuhan
China

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