\documentclass[12pt]{article}
%\usepackage{latex2html}
\usepackage{enumerate}
\usepackage{longtable}
\usepackage{hyperref}
\usepackage{amsmath}
\usepackage{color}
\parindent=0pt
\parskip=12pt
\textheight=24cm
\textwidth=18cm
\topmargin=-2.5cm
\oddsidemargin=-0.5cm
\setcounter{secnumdepth}{5}
\setcounter{tocdepth}{5}
\begin{document}
\sloppy

\title{XDRF2PDB, XDRF2PDB-M, XDRF2X\\
Programs to convert compressed Cartesian coordinate files from UNRES into ASCII formats}

\author{Department of Molecular Modeling\\ Faculty of Chemistry\\ University of Gdansk\\ Sobieskiego 18\\ 80-952 Gdansk, Poland\\
\\
\\
Scheraga Group\\ Baker Laboratory of Chemistry \\
and Chemical Biology\\ Cornell University\\ Ithaca, NY 14853-1303, USA}

\maketitle

%
%TABLE OF CONTENTS
%
%1. License terms
%2. Programs and their functions
%3. Installation
%4. Command lines and files
%	4.1 xdrf2pdb
%	4.2 xdrf2pdb-m
%	4.3 xdrf2x
%	4.4 xdrf2ang
%5. Support
%
\newpage

\section{LICENSE TERMS}
\label{sect:license}

\begin{itemize}

\item
		This software is provided free of charge to academic users, subject to the condition that no part of it be sold or used otherwise for commercial purposes, including, but not limited to its incorporation into commercial software packages, without written consent from the authors. For permission contact Prof. H. A. Scheraga, Cornell University.

\item
		This software package is provided on an ``as is'' basis. We in no way warrant either this software or results it may produce.

\item
		Reports or publications using this software package must contain an acknowledgment to the authors and the NIH Resource in the form commonly used in academic research.

\end{itemize}

\newpage

\section{PROGRAMS AND THEIR FUNCTONS}
\label{sect:programs}

The following three programs can be used to extract conformations from compressed Cartesian (cx) files from UNRES:

\begin{description}

\item{xdrf2pdb} --- takes a single trajectory file and converts it into PDB format.

\item{xdrf2pdb-m} -- takes a multiple-trajectory file from UNRES/MREMD simulations and enables the user to extract conformation of a particular trajectory and save them to a PDB file.

\item{xdrf2x} -- takes a single trajectory file and converts it into UNRES Cartesian coordinate (x) format.

\item{xdrf2ang} -- takes a single trajectory file and calculates UNRES backbone angles (theta and gamma).

\end{description}

\section{INSTALLATION}
\label{sect:install}

Run make all on your system to install all programs or make {\it program} to install a particular program. You might need to run make in the xdrf subdirectory beforehand or point to the xdrf library that is on another directory in the Makefile.

The programs compile on all known Fortran compilers, including gfortran.

\section{COMMAND LINE AND FILES}
\label{sect:command}

For xdrf2pdb and xdrf2pdb-m, you'll need to prepare the UNRES sequence file in either one- or three-letter code.

\subsection{XDRF2PDB}
\label{sect:command:xdrf2pdb}

Command line syntax:

xdrf2pdb one/three seqfile cxfile [freq] [start] [end] [pdbfile]

\begin{description}

\item{one or three} indicates in what format the sequence will be read
\item{seqfile} -- the file with the sequence:
\begin{itemize}
\item one-letter format: 80A1
\item three-letter format: 20(A3,1X)
\end{itemize}
Note that the sequence must match exactly the UNRES sequence.
\item{cxfile} -- full name of the trajectory file with compressed Cartesian coordinates.
\item{freq} (1) -- conformation sampling frequency (each freq-th conformation will be saved to PBD file.
\item{start} (1) -- the first conformation to be saved to PDB file.
\item{end} (1000000000) -- the last conformation to be saved to PDB file.
\item{pdbfile} (cxfile with extension changed from cx to pdb) -- the output PDB file.

\end{description}

\subsection{XDRF2PDB-M}
\label{sect:command:xdrf2pdb-m}

Command line syntax:

xdrf2pdb-m one/three seqfile cxfile [ntraj] [itraj] [pdbfile] [ifreq]

\begin{description}

\item{cxfile} - the name of the compressed trajectory file from an UNRES/MREMD run carried out with TRAJ1FILE (conformations from all trajectories output to a single file).
\item{ntraj} (1) -- number of trajectories in the multi-trajectory run.
\item{itraj} (1) -- the number of trajectory to be extracted.

\end{description}

\subsection{XDRF2X}
\label{sect:command:xdrf2x}

Command line syntax:

xdrf2x cxfile [is] [ie] [freq] $>$ x\_file

The meaning of the the arguments is as in section 
\ref{sect:command:xdrf2pdb}; the conformations are output in UNRES Cartesian coordinate format to stdout.

\subsection{XDRF2ANG}
\label{sect:command:xdrf2ang}

Command line syntax:

xdrf2ang one/three seqfile cxfile [freq] [start] [end] [angfile]

The meaning of the first six parameters is as in section \ref{sect:command:xdrf2pdb} angfile is
	the name of the output angle file; is assigned cx file name with the cx
	extension changed to ang, if not present.

\section{SUPPORT}
\label{sect:support}

   Dr. Adam Liwo\\
   Faculty of Chemistry, University of Gdansk\\
   ul. Sobieskiego 18, 80-952 Gdansk Poland.\\
   phone: +48 58 523 5430\\
   fax: +48 58 523 5472\\
   e-mail: \href{mailto:adam@chem.univ.gda.pl}{\textcolor{blue}{adam@chem.univ.gda.pl}}\\



   Dr. Cezary Czaplewski\\
   Faculty of Chemistry, University of Gdansk\\
   ul. Sobieskiego 18, 80-952 Gdansk Poland.\\
   phone: +48 58 523 5430\\
   fax: +48 58 523 5472\\
   e-mail: \href{mailto:czarek@chem.univ.gda.pl}{czarek@chem.univ.gda.pl}

Prepared by Adam Liwo, 11/26/11

\LaTeX version, 09/28/12

\end{document}
