X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=doc%2FXDRFPDB.TXT;fp=doc%2FXDRFPDB.TXT;h=0000000000000000000000000000000000000000;hp=f2667200690f4ee57f7842d572d0f5396206d5f8;hb=2a226bfc86eabc6e4eae0c3ad1cbc3cb5417a05a;hpb=a0e685f844163003749ba91dfbf4644bcc8cfa30 diff --git a/doc/XDRFPDB.TXT b/doc/XDRFPDB.TXT deleted file mode 100644 index f266720..0000000 --- a/doc/XDRFPDB.TXT +++ /dev/null @@ -1,160 +0,0 @@ - XDRF2PDB, XDRF2PDB-M, XDRF2X - programs to convert compressed - Cartesian coordinate files from UNRES into ASCII formats - ------------------------------------------------------------ - -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 - -1. LICENSE TERMS ----------------- - -* 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. - -* This software package is provided on an "as is" basis. We in no way warrant - either this software or results it may produce. - -* 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. - -2. PROGRAMS AND THEIR FUNCTONS ------------------------------- - -The following three programs can be used to extract conformations from -compressed Cartesian (cx) files from UNRES: - -xdrf2pdb - takes a single trajectory file and converts it into PDB format. - -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. - -xdrf2x - takes a single trajectory file and converts it into UNRES Cartesian - coordinate (x) format - -xdrf2ang - takes a single trajectory file and calculates UNRES backbone - angles (theta and gamma). - -3. INSTALLATION ---------------- - -Run make all on your system to install all programs or make -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 program compiles on all known Fortran compilers, including gfortran. - -4. COMMAND LINE AND FILES -------------------------- - -For xdrf2pdb and xdrf2pdb-m, you'll need to prepare the UNRES sequence file -in either one- or three-letter code. - -4.1 XDRF2PDB - -Command line syntax: - -xdrf2pdb one/three seqfile cxfile [freq] [start] [end] [pdbfile] - -where - -one or three indicates in what format the sequence will be read - -seqfile - the file with the sequence: - -one-letter format: 80A1 - -three-letter format: 20(A3,1X) - -Note that the sequence must match exactly the UNRES sequence - -cxfile - full name of the trajectory file with compressed Cartesian coordinates. - -freq (1) - conformation sampling frequency (each freq-th conformation will - be saved to PBD file - -start (1) - the first conformation to be saved to PDB file - -end (1000000000) the last conformation to be saved to PDB file - -pdbfile (cxfile with extension changed from cx to pdb) - the output PDB file - -4.2 XDRF2PDB-M - -Command line syntax: -xdrf2pdb-m xdrf2pdb-m one/three seqfile cxfile ntraj itraj [pdbfile] [freq] - -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) - -ntraj - number of trajectories in the multi-trajectory run - -itraj - the number of trajectory to be extracted - -pdbfile - (cxfile-without-cx-itraj.pdb) the name of file to write the Cartesian - coordinates of trajectory itraj to - -freq (1) - output frequency - -The xdrf2pdb program to convert cx files to pdb files - -The source is in xdrf2pdb; it requires the libraries in xdrf - -4.3 XDRF2X - -Command line syntax: - -xdrf2x cxfile [is] [ie] [freq] > x_file - -The meaning of the the arguments is as in section 4.1; the conformations -are output in UNRES Cartesian coordinate format to stdout. - -4.4. XDRF2ANG - -Command line syntax: - -xdrf2ang one/three seqfile cxfile [freq] [start] [end] [angfile] - -The meaning of the first six parameters is as in section 4.1; angfile is -the name of the output angle file; is assigned cx file name with the cx -extension changed to ang, if not present. - -5. 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: 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: czarek@chem.univ.gda.pl - -Prepared by Adam Liwo, 11/26/11