In addition, you will need to provide the following input for

charmm2lammps.pl:

1) a CHARMM parameter file (par_<forcefield>.prm)

2) a CHARMM topology file (top_<forcefield>.rtf)

3) a CHARMM coordinates file or pdb file (<project>.crd or <project>.pdb)

   (NOTE: a .pdb file is required if the -cmap option is used)

4) a CHARMM psf file (<project>.psf)

To use the charmm2lammps.pl script, type: "perl charmm2lammps.pl

[-option[=#]] <forcefield> <project>" where <forcefield> is the name

of the CHARMM FF you are using, (i.e. all22_prot), and <project> is

the common name of your *.crd and *.psf files. The options for the

script are listed below. If the option requires a parameter, the

syntax must be [-option[=#]], (i.e. -border=5).

-help        "display available options",                                    

-charmm      "add charmm types to LAMMPS data file",                    

-water       "add TIP3P water [default: 1 g/cc]",                       

-ions        "add (counter)ions using Na+ and Cl- [default: 0 mol/l]",  

-center      "recenter atoms",                                          

-quiet       "do not print info",                                       

-pdb_ctrl    "output project_ctrl.pdb",                                 

-l           "set x-, y-, and z-dimensions simultaneously",             

-lx          "x-dimension of simulation box",                           

-ly          "y-dimension of simulation box",                           

-lz          "z-dimension of simulation box",                           

-border      "add border to all sides of simulation box [default: 0 A]",

-ax          "rotation around x-axis",                                  

-ay          "rotation around y-axis",                                  

-az          "rotation around z-axis"                                   

<forcefield> <project> [-option=value ...]" where <forcefield> is the

name of the CHARMM FF you are using, (i.e. all22_prot), and <project>

is the common name of your *.crd and *.psf files.  Possible options

are listed next.  If the option requires a parameter, the syntax

should be -option=value (e.g. -border=5).

-help        display available options

-charmm      add charmm types to LAMMPS data file

-water       add TIP3P water [default: 1 g/cc]

-ions        add (counter)ions using Na+ and Cl- [default: 0 mol/l]

-center      recenter atoms

-quiet       do not print info

-pdb_ctrl    output project_ctrl.pdb

-l           set x-, y-, and z-dimensions simultaneously

-lx          x-dimension of simulation box

-ly          y-dimension of simulation box

-lz          z-dimension of simulation box

-border      add border to all sides of simulation box [default: 0 A]

-ax          rotation around x-axis

-ay          rotation around y-axis

-az          rotation around z-axis           

-cd          correction for dihedral for carbohydrate systems

-cmap        add CMAP section to data file and fix cmap command lines in 

               input script" (NOTE: requires use of *.pdb file)

In the "example" folder, you will find example files that were created

by following the steps below. These steps describe how to take a

after the # sign is a comment) for user convenience in tracking atom

types etc. according to CHARMM nomenclature.   

The example molecule provided above (i.e., 1ac7) is a DNA fragment.

If instead, a peptide longer than 2 amino acid residues or a protein

is to be modeled, the '-cmap' option should be used. This will add a

section at the end of the data file with the heading of 'CMAP' that

will contain cmap crossterm corrections for the phi-psi dihedrals for

the amino acid residues. You will then need to also copy the

appropriate file for the cmap crossterms into your directory and be

sure that you are using the appropriate cmap crossterms that go with

the respective version of the charmm force field that is being used

(e.g, cmap22.data or cmap36.data). This is necessary to account for

the fact that the CHARMM group has provided updated cmap correction

terms for use with the c36 and more recent version of the charmm

protein force field.  Copies of cmap22.data and cmap36.data are

provided in the tools/ch2lmp directory.

The default timestep in the LAMMPS *.in file is set to 0.5 fs, which

can typically be increased to 2 fs after equilibration if the bonds

involving H are constrained via shake. Also, after equilibration, the

speed.

The -ions option allows the user to neutralize the simulation cell

with Na+ or Cl- counterions if the molecule has a net

charge. Additional salt can be added by increasing the default

concentration (i.e. -ions=0.5).

with Na+ or Cl- counterions if the molecule has a net charge

Additional salt can be added by increasing the default concentration

(e.g. -ions=0.5).

** In the "other" file folder, you will find:

3) A 3rd party perl script called "crd2pdb.pl"

4) A 3rd party fortran code called "pdb_to_crd.f"