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

Laboratory of Molecular Modeling
Faculty of Chemistry
University of Gdansk
Wita Stwosza 63
80-308 Gdansk, Poland

Scheraga Group
Baker Laboratory of Chemistry
and Chemical Biology
Cornell University
Ithaca, NY 14853-1301, USA

December 4, 2014

Contents

• 1 LICENSE TERMS
• 2 PROGRAMS AND THEIR FUNCTONS
• 3 INSTALLATION
• 4 COMMAND LINE 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 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. It is recommeded to use Cmake
to install whole package; please see Installation Guide.

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]

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 one/three seqfile cxfile [ntraj] [itraj] [pdbfile] [ifreq]

 

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 (1) - number of trajectories in the multi-trajectory run.

 

itraj (1) - the number of trajectory to be extracted.

 

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. Wita Stwosza 63, 80-308 Gdansk Poland.
phone: +48 58 523 5124
fax: +48 58 523 5012
e-mail: adam(at)sun1.chem.univ.gda.pl

Dr. Cezary Czaplewski
Faculty of Chemistry, University of Gdansk
ul. Wita Stwosza 63, 80-308 Gdansk Poland.
phone: +48 58 523 5126
fax: +48 58 523 5012
e-mail: cezary.czaplewski(at)ug.edu.pl

Prepared by Adam Liwo, 11/26/11
L^ATEXversion, 09/28/12
Revised by Adam Liwo, 12/04/14

This manual is available in the PDF format also.