This directory contains example CHARMM input files that allow the user to
replicate the parameterization of pyrrolidine as described in the paper
/----------------------------------------------------------------------------\
| CHARMM General Force Field (CGenFF): a force field for drug-like molecules |
| compatible with the CHARMM all-atom additive biological force fields       |
\----------------------------------------------------------------------------/
by K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim,
E. Darian, O. Guvench, P. Lopes, I. Vorobyov, and A. D. MacKerell Jr.

It contains the following files:
FILE_ID.DIZ                    608 ASCII English text
    ....general information about this directory

README.txt                     641 ASCII English text
    ....README file as required by JCC

extract_tutorial               521 POSIX shell script text executable
    ....script to extract information from the Gaussian MP2 PES in the 
framework of the tutorial

files.descr                   4088 ASCII English text
    ....description of the different files in this directory

gauss                         4096 directory
    ....directory with inputs and outputs of Gaussian MP2 minimization and 
water interaction

gausst1                       4096 directory
    ....directory with input and output of 1st Gaussian MP2 PES

gausst2                       4096 directory
    ....directory with input and output of 2nd Gaussian MP2 PES

gausst3                       4096 directory
    ....directory with input and output of 3rd Gaussian MP2 PES

gausst4                       4096 directory
    ....directory with input and output of 4th Gaussian MP2 PES

generate.inp                  2275 ASCII text
    ....CHARMM script that generates the 3D structure of a model compound and 
creates a Gaussian input

generate_tutorial.inp         2688 ASCII English text
    ....CHARMM script that generates the 3D structure of a model compound in 
the framework of the tutorial

prld_min_orient.pdb           1284 ASCII text
    ....CHARMM minimized structure of pyrrolidine, aligned with its MP2 geometry

prld_missing1.txt              855 ASCII text
    ....missing bond and valence angle parameters after initially generating 
pyrrolidine

prld_missing2.txt              531 ASCII text
    ....missing dihedral parameters after generating pyrrolidine

prld_molvib_qm.inp           19115 ASCII English text
    ....CHARMM script that performes the PED analysis on a Gaussian vibrational 
spectrum

prld_molvib_qm.out            5224 ASCII English text
    ....PED analysis on pyrrolidine's MP2 vibrational spectrum

prld_mp2.crd                  1990 ASCII text
    ....CHARMM crd file with the MP2 optimized structure of pyrrolidine

prld_water.ene                1449 ASCII text
    ....water interaction energies and distances after optimizing pyrrolidine

quick_molvib.inp              7468 ASCII English text
    ....CHARMM script that performs measurements on the CHARMM equilibrium 
geometry of a model compound and also performes PED analysis

quick_molvib1.out            34090 ASCII English text
    ....measurements and PED analysis after the 4th step of the 
parameterization procedure (see tutorial.html)

quick_molvib2.out            34019 ASCII English text
    ....measurements and PED analysis after the 5th step of the 
parameterization procedure (see tutorial.html)

quick_molvib_tutorial.inp     7771 ASCII English text
    ....CHARMM script that performs measurements and PED analysis in the 
framework of the tutorial

run_pes                        664 POSIX shell script text executable
    ....script to extract information from the Gaussian MP2 PES, pass in on to 
CHARMM, run the corresponding CHARMM PES, and make a plot using GnuPlot

scan                          4096 directory
    ....directory with input for CHARMM PES

toppar_prld1.str              1571 ASCII text
    ....toppar file for pyrrolidine after the 1st step of the parameterization 
procedure (see tutorial.html)

toppar_prld2.str              2432 ASCII text
    ....toppar file for pyrrolidine after the 2nd step of the parameterization 
procedure (see tutorial.html)

toppar_prld3.str              2718 ASCII text
    ....toppar file for pyrrolidine after the 3rd step of the parameterization 
procedure (see tutorial.html)

toppar_prld4.str              2714 ASCII text
    ....toppar file for pyrrolidine after the 4th step of the parameterization 
procedure (see tutorial.html)

toppar_prld5.str              2669 ASCII English text
    ....toppar file for pyrrolidine after the 5th step of the parameterization 
procedure (see tutorial.html)

toppar_prld6.str              2666 ASCII English text
    ....toppar file for pyrrolidine after the 6th step of the parameterization 
procedure (see tutorial.html)

toppar_prld7.str              2658 ASCII text
    ....toppar file for pyrrolidine after the 7th step of the parameterization 
procedure (see tutorial.html)

toppar_prld8.str              2658 ASCII English text
    ....toppar file for pyrrolidine after the 8th step of the parameterization 
procedure (see tutorial.html)

water.inp                    24862 ASCII English text
    ....CHARMM script that calcuates minimized interaction enegies and 
distances between water and a model compound at CHARMM geometry

water_constr.inp             24862 ASCII English text
    ....CHARMM script that calcuates minimized interaction enegies and 
distances between water and a model compound at MP2 geometry

water_constr_tutorial.inp    25218 ASCII English text
    ....CHARMM script that calcuates water interaction energies and distances 
using the MP2 geometry in the framework of the tutorial

water_tutorial.inp           25218 ASCII English text
    ....CHARMM script that calcuates water interaction energies and distances 
using the CHARMM geometry in the framework of the tutorial

