X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=doc%2F3.1%2Fascii-text%2FXDRFPDB.TXT;fp=doc%2F3.1%2Fascii-text%2FXDRFPDB.TXT;h=f2667200690f4ee57f7842d572d0f5396206d5f8;hp=0000000000000000000000000000000000000000;hb=b75425747e3e2b448ca5e0ef8367712e1f339124;hpb=ce0fdb6f6e62a69055ec0f737c339851ee4b43b4 diff --git a/doc/3.1/ascii-text/XDRFPDB.TXT b/doc/3.1/ascii-text/XDRFPDB.TXT new file mode 100644 index 0000000..f266720 --- /dev/null +++ b/doc/3.1/ascii-text/XDRFPDB.TXT @@ -0,0 +1,160 @@ + 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