Global optimization of biomolecules using AMBER9

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 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!