Adk44: Created page with "Here you can find examples of input files necessary to work with GMIN: 1. ''coords.inpcrd'' -- file with coordinates 2. ''coords.prmtop'' -- topology file (see [http://wwmm...."

2019-05-10T17:08:01Z

Created page with "Here you can find examples of input files necessary to work with GMIN: 1. ''coords.inpcrd'' -- file with coordinates 2. ''coords.prmtop'' -- topology file (see [http://wwmm...."

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Here you can find examples of input files necessary to work with GMIN:

1. ''coords.inpcrd'' -- file with coordinates

2. ''coords.prmtop'' -- topology file (see [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Perm-prmtop.py here])

3. ''min.in'' -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system, however in this particular case AMBER9 calculates only energy of the system, e.g.:

# Minimization Parameters
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 2, saltcon=0.1,
ntb = 0,
cut = 8.22,
rgbmax = 8.22,
ifswitch = 1,
/

4. ''min_md.in'' -- this file controls conditions for molecular dynamics in AMBER9, e.g.:

# MD Paramaters
&cntrl
imin = 0,
tempi = 0.0, temp0 = 400.0,
ntt = 3, gamma_ln = 10.0,
nstlim = 500, dt = 0.001,
igb = 2, saltcon = 0.1,
ntb = 0,nscm=0,
ntc = 2,ntf = 2,
ntpr = 500, ntwx = 500, ntwr=500,
nrespa=1,
cut = 999.0,
rgbmax = 8.22,
ifswitch = 1,
/

For the MD steps, imin=0, no minisations are performed. and no cutoffs cut = 999.0 should be used.

Also igb=2 means that we are using the 2nd GB models is expected to perform well on proteins.

saltcon=0.2 sets the surrounding (monovalent) salt concentration to 0.2 [mol/L].

tempi = 0 sets the initial temperature temp0 = 400 sets final temperature in Kelvin.

.5ps of MD with a 1.0fs time step is set bynstlim=500, dt=0.001

 ntt=3 Langevin dynamics with gamma_ln = 10.0 sets frequency of coupling to heat bath to the collision rate of 10 ps-1

ntpr = 100 Energy output frequency
ntwr = 100 Restart file frequency
ntwx = 100 Trajectory file frequency

 ntb = 0 non-periodic, use cutoff for non-bond

ntc=2, ntf=2, use SHAKE to constrain only H bonds (ntc=2) and omit force evaluations for these bonds (ntf=2).

nrespa=2, take a bigger time stepfor evaluating the slow-varying terms in the force field. In this setting, the time step is equal to nrespa * dt ( 2 * 2 fs = 4 fs.

ntr=1,restraint_wt=30.0, set constraint and strength.

rstraintmask='@N,C,CA', constrain backbone atoms only

5. ''data'' -- file with GMIN keywords:

SLOPPYCONV 1.0D-2
TIGHTCONV 1.0D-3
UPDATES 8000
MAXERISE 0.001
STEPS 100 1.0
STEP 0.00 0.0
AMBER9 coords.inpcrd inpcrd
AMBERMDSTEPS
MAXIT 10000 10000
MAXBFGS 1.0
SAVE 100
TEMPERATURE 1.0
RADIUS 300.0
DUMPSTRUCTURES

Thats all for the beginning!

Global optimization of biomolecules using AMBER9 - Revision history

Adk44: Created page with "Here you can find examples of input files necessary to work with GMIN: 1. ''coords.inpcrd'' -- file with coordinates 2. ''coords.prmtop'' -- topology file (see [http://wwmm...."