AMBER force field parameters

AMBER format PARM file and coordinate file can be read by NAMD, which allows one to use AMBER force field to carry out all types of simulations that NAMD has supported. NAMD can read PARM files in either the format used in AMBER 6 or the new format defined in AMBER 7. The output of the simulation (restart file, DCD file, etc.) will still be in traditional format that has been used in NAMD.

• amber $<$ use AMBER format force field? $>$
  Acceptable Values: yes or no
  Default Value: no
  Description: If amber is set to on, then parmfile must be defined, and structure and parameters should not be defined.

• parmfile $<$ AMBER format PARM file $>$
  Acceptable Values: UNIX filename
  Description: This file contains complete topology and parameter information of the system.

• ambercoor $<$ AMBER format coordinate file $>$
  Acceptable Values: UNIX filename
  Description: This file contains the coordinates of all the atoms. Note that coordinates can also be used for PDB format coordinate file. When amber is set to on, either ambercoor or coordinates must be defined, but not both.

• readexclusions $<$ Read exclusions from PARM file? $>$
  Acceptable Values: yes or no
  Default Value: yes
  Description: PARM file explicitly gives complete exclusion (including 1-4 exclusions) information. When readexclusions is set to on, NAMD will read all exclusions from PARM file and will not add any more; alternatively, if readexclusions is set to off, NAMD will ignore the exclusions in PARM file and will automatically generate them according to the exclusion policy specified by exclude.

• scnb $<$ VDW 1-4 scaling factor $>$
  Acceptable Values: decimal $\geq$ 1.0
  Default Value: 2.0
  Description: Same meaning as SCNB in AMBER. Note that in NAMD, 1-4 vdw interactions are DIVIDED by scnb, whereas 1-4 electrostatic interactions are MULTIPLIED by 1-4scaling. So 1-4scaling should be set to the inverse of SCEE value used in AMBER.

Caveat:

1. Polarizable parameters in AMBER are not supported.

2. NAMD does not support the 10-12 potential terms in some old AMBER versions. When non-zero 10-12 parameter is encountered in PARM file, NAMD will terminate.

3. NAMD has several exclusion policy options, defined by exclude. The way AMBER dealing with exclusions corresponds to the ``scaled1-4'' in NAMD. So for simulations using AMBER force field, one would specify ``exclude scaled1-4'' in the configuration file, and set 1-4scaling to the inverse value of SCEE as would be used in AMBER.

4. NAMD does not read periodic box lengths in PARM or coordinate file. They must be explicitly specified in NAMD configuration file.

5. By default, NAMD applies switching functions to the non-bond interactions within the cutoff distance, which helps to improve energy conservation, while AMBER does not use switching functions so it simply truncates the interactions at cutoff. However, if ``authentic'' AMBER cutoff simulations are desired, the switching functions could be turned off by specifying ``switching off'' in NAMD configuration file.

6. When SHAKE is applied to water molecules, NAMD constrains the two O-H bonds and the H-O-H angle, which produces the same result as constraining the additional H-H bond. But in some AMBER models, water is defined by three real bonds and no angle. In this case NAMD will apply SHAKE only to the two O-H bonds and not to the angle or the H-H bond (because the angle is not defined). Thus, when SHAKE is used along with this kind of water model, difference would be expected between NAMD and AMBER.

7. NAMD and AMBER may have different default values for some parameters (e.g., the tolerance of SHAKE). One should check other sections of this manual for accurate descriptions of the NAMD options.

Following are two examples of the NAMD configuration file to read AMBER force field and carry out simulation. They may help users to select proper NAMD options for AMBER force field. For the convenience of AMBER users, the AMBER 6 sander input files are given in the left for comparison, which would accomplish similar tasks in AMBER.

Example 1: Non-periodic boundary system, cutoff simulation

---AMBER----      ---NAMD---

 TITLE
 &cntrl
  ntb=0, igb=2,   # non-periodic, use cutoff for non-bond
  nstlim=1000,    numsteps       1000  # Num of total steps
  ntpr=50,        outputEnergies 50  # Energy output frequency
  ntwr=50,        restartfreq    50  # Restart file frequency
  ntwx=100,       DCDfreq        100  # Trajectory file frequency
  dt=0.001,       timestep       1  # in unit of fs (This is default)
  tempi=0.,       temperature    0  # Initial temp for velocity assignment
  cut=10.,        cutoff         10
                  switching      off  # Turn off the switching functions
  scee=1.2,       exclude        scaled1-4
                  1-4scaling     0.833333  # =1/1.2, default is 1.0
  scnb=2.0        scnb           2  # This is default
 &end
                  amber          on  # Specify this is AMBER force field
                  parmfile       prmtop  # Input PARM file
                  ambercoor      inpcrd  # Input coordinate file
                  outputname     md  # Prefix of output files

Example 2: Periodic boundary system, PME, NVE ensemble, using SHAKE algorithm

---AMBER----      ---NAMD---

 TITLE
 &cntrl
  ntc=2, ntf=2,   # SHAKE to the bond between each hydrogen and it mother atom
                  rigidBonds     all
  tol=0.0005,     rigidTolerance 0.0005  # Default is  0.00001
  nstlim=500,     numsteps       500  # Num of total steps
  ntpr=50,        outputEnergies 50  # Energy output frequency
  ntwr=100,       restartfreq    100  # Restart file frequency
  ntwx=100,       DCDfreq        100  # Trajectory file frequency
  dt=0.001,       timestep       1  # in unit of fs (This is default)
  tempi=300.,     temperature    300  # Initial temp for velocity assignment
  cut=9.,         cutoff         9
                  switching      off  # Turn off the switching functions
 &end
 &ewald           PME            on  # Use PME for electrostatic calculation
                  # Orthogonal periodic box size
  a=62.23,        cellBasisVector1   62.23  0  0
  b=62.23,        cellBasisVector2   0  62.23  0
  c=62.23,        cellBasisVector3   0  0  62.23
  nfft1=64,       PMEGridSizeX   64
  nfft2=64,       PMEGridSizeY   64
  nfft3=64,       PMEGridSizeZ   64
  ischrgd=1,      # NAMD doesn't force neutralization of charge
 &end
                  amber          on  # Specify this is AMBER force field
                  parmfile       FILENAME  # Input PARM file
                  ambercoor      FILENAME  # Input coordinate file
                  outputname     PREFIX  # Prefix of output files
                  exclude        scaled1-4
                  1-4scaling     0.833333  # =1/1.2, default is 1.0