import updated README file for charmm2lammps.pl with CMAP support

<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).

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

must be like this: -option=value (e.g. -border=5).

-help        display available options

-charmm      add charmm types to LAMMPS data file

-nohints     do not add charmm types and style hints 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

-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)

   1ac7.pdb file.

6) Run charmm2lammps.pl by typing:

"perl charmm2lammps.pl all27_na 1ac7 -charmm -border=1 -pdb_ctrl -water -ions"

"perl charmm2lammps.pl all27_na 1ac7 -border=1 -pdb_ctrl -water -ions"

7) Run lammps by typing: "lmp < 1ac7.in"

7) Run lammps by typing: "lmp_mpi -in 1ac7.in"

8) Run lammps2pdb.pl by typing: "perl lammps2pdb.pl 1ac7"

embeds the molecule in water on a crystal lattice. The -border option

includes a layer of water surrounding the minimum dimensions of the

molecule. The -pdb_ctrl option produces the 1ac7_ctrl.pdb file that

can be visualized in a standard visualization package such as VMD. The

-charmm option put comments into the LAMMPS data file (everything

can be visualized in a standard visualization package such as VMD. By

default, comments are added into the LAMMPS data file (everything

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

types etc. according to CHARMM nomenclature.

types etc. according to CHARMM nomenclature. If this is not desired,

the -nohints option can be used to turn off this function.

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

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

(e.g. -ions=0.5).

(i.e., -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"