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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
The following three programs can be used to extract conformations from compressed Cartesian (cx) files from UNRES:
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.
For xdrf2pdb and xdrf2pdb-m, you'll need to prepare the UNRES sequence file in either one- or three-letter code.
Command line syntax:
xdrf2pdb one/three seqfile cxfile [freq] [start] [end] [pdbfile]
Note that the sequence must match exactly the UNRES sequence.
Command line syntax:
xdrf2pdb-m one/three seqfile cxfile [ntraj] [itraj] [pdbfile] [ifreq]
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.
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.
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
LATEXversion, 09/28/12
Revised by Adam Liwo, 12/04/14
This manual is available in the PDF format also.