clarify ch2lmp commands purpose in tools section

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 a

PDB file with associated CHARMM info, including CHARMM force field

data, into its LAMMPS equivalent.  Using lammps2pdb.pl you can convert

LAMMPS atom dumps into PDB files.

data, into its LAMMPS equivalent. Support for the CMAP correction of

CHARMM22 and later is available as an option. This tool can also add

solvent water molecules and Na+ or Cl- ions to the system.

Using lammps2pdb.pl you can convert LAMMPS atom dumps into PDB files.

See the README file in the ch2lmp sub-directory for more information.

These tools were created by Pieter in't Veld (pjintve at sandia.gov)

and Paul Crozier (pscrozi at sandia.gov) at Sandia.

CMAP support added and tested by Xiaohu Hu (hux2 at ornl.gov) and

Robert A. Latour (latourr at clemson.edu), David Hyde-Volpe, and

Tigran Abramyan, (Clemson University) and

Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.

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chain tool :h4,link(chain)

The charmm2lmp sub-directory contains tools for converting files back-and-forth between

the CHARMM MD code and LAMMPS.

The charmm2lammps.pl perl script converts CHARMM input files into LAMMPS input.

The lammps2pdb.pl perl script converts LAMMPS dump files into a pdb series file.

The mkpdb.f fortran 90 code also converts LAMMPS dump files into PDB files, and the 

mkdcd.f tool converts LAMMPS dump files into CHARMM *.dcd trajectory files that can

be read-in to CHARMM for analysis. See the README file in the charmm2lmp sub-directory

for more information.

These tools were written by Pieter J. in 't Veld (pjintve@sandia.gov) and Paul Crozier

(pscrozi@sandia.gov) at Sandia.

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