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example
other
README
charmm2lammps.pl
lammps2pdb.pl
main_manual

README

These tools were created by Pieter J. in 't Veld (pjintve@sandia.gov)
and Paul Crozier (pscrozi@sandia.gov), Sandia National Laboratories,
2005. They are intended to make it easy to use CHARMM as a builder and
as a post-processor for LAMMPS. Using charmm2lammps.pl, you can
convert an ensemble built in CHARMM into its LAMMPS equivalent.  Using
lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files.

In this directory, you should find:
1) A perl script called "charmm2lammps.pl"
2) A perl script called "lammps2pdb.pl"
3) An "example" folder containing an example of how to use these tools.
4) An "other" folder containing other potentially useful tools.

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)
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"                                   

In the "example" folder, you will find example files that were created
by following the steps below. These steps describe how to take a
biomolecule and convert it into LAMMPS input, and then create a *.pdb
trajectory from the LAMMPS output.

1) Get the pdb file you want to model. http://www.rcsb.org/pdb/ For
this example, we will use 1ac7.pdb

2) If there are multiple models in the pdb file, choose the one you
want and delete the others. Save the pared-down file as 1ac7_pared.pdb

3) Download the charmm FF files and choose the one you want from the
tarball.  We will use all27_na for this example.
http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm
toppar_c31b1.tar.gz

4) Create a *.pgn file for use with psfgen (you will need to have VMD
installed, http://www.ks.uiuc.edu/Research/vmd/ ). This is the hardest
step because you have to change the residue names from what the *.pdb
file has to the corresponding names in the charmm FF files. You'll
need to add a "pdbalias residue x xnew" line for each change that
needs to be made.  The *.pgn should contain something like this:

package require psfgen   
topology top_all27_na.rtf
pdbalias residue A ADE 
pdbalias residue T THY 
pdbalias residue G GUA 
pdbalias residue C CYT 
.
.
.
segment A {pdb 1ac7_pared.pdb}   
coordpdb 1ac7_pared.pdb A   
guesscoord   
writepdb 1ac7.pdb   
writepsf charmm 1ac7.psf  
exit 

5) Type "vmd -e 1ac7.pgn" to build the 1ac7.psf file, and the new
   1ac7.pdb file.

6) Run charmm2lammps.pl by typing: 
"perl charmm2lammps.pl all27_na 1ac7 -charmm -border=1 -pdb_ctrl -water -ions"

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

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

** Additional notes:

The charmm2lammps.pl script takes the pdb and psf files for the 1ac7
molecule and converts them into LAMMPS format. The -water option
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
after the # sign is a comment) for user convenience in tracking atom
types etc. according to CHARMM nomenclature.

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
delay on neigh_modify can probably increased to 5 or so to improve
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).

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

1) A FORTRAN 90 code called "mkpdb.f". Requires "in_mkpdb".  This is a
   fortran code that is an alternative way to convert LAMMPS dump
   files into pdb format.

2) A FORTRAN 90 code called "mkdcd.f" (and a FORTRAN 77 version called
   mkdcd_f77.f).  Requires "in_mkdcd". Creates CHARMM format
   trajectories from LAMMPS dump files.

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

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


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