This directory contains supplementary material for
/----------------------------------------------------------------------------\
| 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:
3pomp                         4096 directory
    ....directory with everything needed to to replicate the parameterization 
of 3-phenoxymethylpyrrolidine

3pomp.txt                     2186 ASCII C++ program text
    ....CHARMM residue topology entry for 3-phenoxymethylpyrrolidine

3pomp_scan.png               31069 PNG image data, 364 x 244, 8-bit/color RGBA, non-interlaced
    ....3-phenoxymethylpyrrolidine PES before and after optimization; part of 
the tutorial

3pomperr.txt                  1041 ASCII text
    ....CHARMM "missing parameter" errors for 3-phenoxymethylpyrrolidine

FILE_ID.DIZ                    513 ASCII English text
    ....general information about this directory

README.txt                     546 ASCII English text
    ....README file as required by JCC

atlist.txt                    6869 ASCII C program text
    ....list of CGenFF atom types

c34b1cgenffpatch.tgz         28418 gzip compressed data, from Unix, last modified: Wed Oct  8 17:36:30 2008
    ....patch that enables CHARMM 34b1 to read in CGenFF files; untar into 
c34b1 directory and re-compile

c34b2cgenffpatch.tgz         28383 gzip compressed data, from Unix, last modified: Tue Apr  1 17:05:22 2008
    ....patch that enables CHARMM 34b2 to read in CGenFF files; untar into 
c34b2 directory and re-compile

c35a1cgenffpatch.tgz         28223 gzip compressed data, from Unix, last modified: Thu Jan 24 15:48:30 2008
    ....patch that enables CHARMM 35a1 to read in CGenFF files; untar into 
c35a1 directory and re-compile

c35a2cgenffpatch.tgz         28558 gzip compressed data, from Unix, last modified: Tue Apr  1 17:05:07 2008
    ....patch that enables CHARMM 35a2 to read in CGenFF files; untar into 
c35a2 directory and re-compile

do_remas                       340 POSIX shell script text executable
    ....script that processes CGenFF rtf and prm files so that they can be used 
together with CHARMM22 protein FF

figure1web.png               19002 PNG image data, 400 x 341, 8-bit gray+alpha, non-interlaced
    ....low-resolution version of figure 1 in the paper for embedding in the 
tutorial

figure2web.png               35900 PNG image data, 300 x 315, 8-bit/color RGBA, non-interlaced
    ....low-resolution version of figure 2 in the paper for embedding in the 
tutorial

figure3web.png               25323 PNG image data, 252 x 167, 8-bit/color RGBA, non-interlaced
    ....low-resolution version of figure 3 in the paper for embedding in the 
tutorial

figure5web.png                6478 PNG image data, 258 x 236, 8-bit gray+alpha, non-interlaced
    ....low-resolution version of figure 5 in the paper for embedding in the 
tutorial

files.descr                   3691 ASCII English text
    ....description of the different files in this directory

genreadme                      336 POSIX shell script text executable
    ....script that generates README.txt from FILE_ID.DIZ and files.descr

mispar                        1691 POSIX shell script text executable
    ....script that extracts "MISSING PARAMETER" entries from a CHARMM output 
and finds analogous parameters

outliers                      4096 directory
    ....directory with geometries of most important outliers in figure 7

par_all22_prot.prm          169200 ASCII English text
    ....CHARMM22 protein parameter file with "MASS" entries from 
top_all22_prot.rtf to make it work with "FLEX"

par_all36_cgenff.prm        441466 ASCII English text
    ....CGenFF parameter file

pes                           3801 python script text executable
    ....script that extracts geometries and energies from a Gaussian PES (by 
Olgun Guvench)

prld_scan_init.png           23478 PNG image data, 368 x 244, 8-bit/color RGBA, non-interlaced
    ....pyrrolidine PES before optimization as produced by gnuplot; part of the 
tutorial

prld_scan_opt.png            23506 PNG image data, 368 x 244, 8-bit/color RGBA, non-interlaced
    ....pyrrolidine PES after optimization as produced by gnuplot; part of the 
tutorial

pyrrolidine                   4096 directory
    ....directory with example CHARMM scripts that allow the user to replicate 
the parameterization of pyrrolidine

rawdata_fig7-10.ods          70496 data
    ....spreadsheet with raw data behind figures 7, 8 and 10 - Openoffice.org 
version

rawdata_fig7-10.xls         246784 Microsoft Office Document
    ....spreadsheet with raw data behind figures 7, 8 and 10 - Microsoft Excel 
version

remas                          165 awk script text executable
    ....script that renumbers "MASS" entries in rtf and prm files

remove_pyrrolidine             227 POSIX shell script text executable
    ....scripts that removes pyrrolidine from the CGenFF topology and parameter 
files for tutorial

rm_pyrrolidine_remas           251 POSIX shell script text executable
    ....scripts that removes pyrrolidine from CGenFF topology and parameter 
files processed by "remas"

scanplot                       736 POSIX shell script text executable
    ....script that plots the result of a CHARMM PES using GnuPlot

sleight.js                     982 ASCII C++ program text, with CRLF line terminators
    ....script that makes old Internet Explorer versions render transparent png 
files correctly

top_all22_prot.rtf           74260 ASCII English text
    ....standard CHARMM22 protein residue topology file

top_all36_cgenff.rtf       1151691 ASCII English text
    ....CGenFF residue topology file

toppar_dum_nobel_gases.str    1594 ASCII English text
    ....CHARMM22 stream file for dummy atoms and noble gases with "FLEX" keyword

tutorial.html                58157 HTML document text
    ....HTML tutorial

