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19 \title{XDRF2PDB, XDRF2PDB-M, XDRF2X\\
20 Programs to convert compressed Cartesian coordinate files from UNRES into ASCII formats}
22 \author{Department of Molecular Modeling\\ Faculty of Chemistry\\ University of Gdansk\\ Sobieskiego 18\\ 80-952 Gdansk, Poland\\
25 Scheraga Group\\ Baker Laboratory of Chemistry \\
26 and Chemical Biology\\ Cornell University\\ Ithaca, NY 14853-1303, USA}
34 %2. Programs and their functions
36 %4. Command lines and files
45 \section{LICENSE TERMS}
51 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.
54 This software package is provided on an ``as is'' basis. We in no way warrant either this software or results it may produce.
57 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.
63 \section{PROGRAMS AND THEIR FUNCTONS}
66 The following three programs can be used to extract conformations from compressed Cartesian (cx) files from UNRES:
70 \item{xdrf2pdb} --- takes a single trajectory file and converts it into PDB format.
72 \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.
74 \item{xdrf2x} -- takes a single trajectory file and converts it into UNRES Cartesian coordinate (x) format.
76 \item{xdrf2ang} -- takes a single trajectory file and calculates UNRES backbone angles (theta and gamma).
80 \section{INSTALLATION}
83 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.
85 The programs compile on all known Fortran compilers, including gfortran.
87 \section{COMMAND LINE AND FILES}
90 For xdrf2pdb and xdrf2pdb-m, you'll need to prepare the UNRES sequence file in either one- or three-letter code.
93 \label{sect:command:xdrf2pdb}
97 xdrf2pdb one/three seqfile cxfile [freq] [start] [end] [pdbfile]
101 \item{one or three} indicates in what format the sequence will be read
102 \item{seqfile} -- the file with the sequence:
104 \item one-letter format: 80A1
105 \item three-letter format: 20(A3,1X)
107 Note that the sequence must match exactly the UNRES sequence.
108 \item{cxfile} -- full name of the trajectory file with compressed Cartesian coordinates.
109 \item{freq} (1) -- conformation sampling frequency (each freq-th conformation will be saved to PBD file.
110 \item{start} (1) -- the first conformation to be saved to PDB file.
111 \item{end} (1000000000) -- the last conformation to be saved to PDB file.
112 \item{pdbfile} (cxfile with extension changed from cx to pdb) -- the output PDB file.
116 \subsection{XDRF2PDB-M}
117 \label{sect:command:xdrf2pdb-m}
121 xdrf2pdb-m one/three seqfile cxfile [ntraj] [itraj] [pdbfile] [ifreq]
125 \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).
126 \item{ntraj} (1) -- number of trajectories in the multi-trajectory run.
127 \item{itraj} (1) -- the number of trajectory to be extracted.
132 \label{sect:command:xdrf2x}
136 xdrf2x cxfile [is] [ie] [freq] $>$ x\_file
138 The meaning of the the arguments is as in section
139 \ref{sect:command:xdrf2pdb}; the conformations are output in UNRES Cartesian coordinate format to stdout.
141 \subsection{XDRF2ANG}
142 \label{sect:command:xdrf2ang}
146 xdrf2ang one/three seqfile cxfile [freq] [start] [end] [angfile]
148 The meaning of the first six parameters is as in section \ref{sect:command:xdrf2pdb} angfile is
149 the name of the output angle file; is assigned cx file name with the cx
150 extension changed to ang, if not present.
156 Faculty of Chemistry, University of Gdansk\\
157 ul. Sobieskiego 18, 80-952 Gdansk Poland.\\
158 phone: +48 58 523 5430\\
159 fax: +48 58 523 5472\\
160 e-mail: \href{mailto:adam@chem.univ.gda.pl}{\textcolor{blue}{adam@chem.univ.gda.pl}}\\
164 Dr. Cezary Czaplewski\\
165 Faculty of Chemistry, University of Gdansk\\
166 ul. Sobieskiego 18, 80-952 Gdansk Poland.\\
167 phone: +48 58 523 5430\\
168 fax: +48 58 523 5472\\
169 e-mail: \href{mailto:czarek@chem.univ.gda.pl}{czarek@chem.univ.gda.pl}
171 Prepared by Adam Liwo, 11/26/11
173 \LaTeX version, 09/28/12