Using BHINTERP to find minima between two end points

When using AMBER9

On the beginning you need to have two optimized structures which are called endpoints. Often they are the initial and final structures of studied path or reaction (however, here reaction means geometrical change in the system, not breaking and forming new bonds).

What files do you need to find a path connecting both endpoints?

1. coords.inpcrd -- file with coordinates in AMBER9 format (it can contain geometry of one of the endpoints)

2. coords.prmtop -- AMBER9 topology file prepared according to information presented [Link here]

3. min.in - file with AMBER9 keywords describing the conditions for molecular dynamics of the studied system, e.g.:

 Minimization
 &cntrl
    imin=1, maxcyc=1, ncyc=1,
    igb=2, saltcon=0.2,
    ntx=1, ntb=0,
    cut=15.0, rgbmax=12.0, ifswitch=1
  /

4. start -- file with x, y, z coordinates of the first endpoint

5. finish -- file with x, y, z coordinates of the second endpoint

6. start.1 which is a copy of start

7. finish.2 -- a copy of finish

8. odata.bhinterp -- file with OPTIM keywords specifying method of searching of minima, convergence criterion, etc. e.g.:

  MAXBFGS     1.0
  MAXERISE    1.0D-4
  EDIFFTOL    1.0D-6
  GEOMDIFFTOL 0.1
  BFGSMIN     1.0D-6
  BFGSSTEPS   10000
  NOFRQS
  DUMPDATA
  PERMDIST
  AMBER9 start
  POINTS

NOFRQS is specially useful for large system, a few thousands atoms, where calculation of frequencies is too time consuming. For smaller system you can use ...

9. pathdata -- in this file all necessary PATHSAMPLE keywords should be put:

  EXEC /home/wales/bin/A9OPTIM.4.0
  TEMPERATURE 0.592
  NATOMS      2923
  TRIPLES
  ADDTRIPLES
  JOBSPERNODE 1
  CYCLES      1000
  ITOL        1.0D0
  GEOMDIFFTOL 0.1
  EDIFFTOL    1.0D-6
  PERMDIST
  DIJINITSTART EXP
  COPYOPTIM
  COPYFILES perm.allow min.in coords.inpcrd coords.prmtop
  COMMENT  thresh  maxe     BHsteps    RMS   T     step-size accrat   K   sfrac
  BHINTERP    5   -9100.0      1      0.01  1.00    0.4      0.5   10.0   0.5
  AMBER9

Take care to change path to executable, NATOMS and maxe (the second parameter in BHINTERP, it should/can be about 200 smaller than energies of both endpoints). Line 'JOBSPERNODE 1' is necessary for parallel jobs. If keyword PERMDIST is present you need to have in the same directory file with a list of all atom pairs or groups which can be permuted.

10. perm.allow -- file with list atoms that may be permuted. Information how to get this file you can find Link here.