--- /dev/null
+ WHAM (Weighted Histogram Analysis Method)
+ Processing results of UNRES/MREMD simulations
+ ---------------------------------------------
+
+TABLE OF CONTENTS
+-----------------
+
+1. License terms
+
+2. References
+
+3. Functions of the program
+
+4. Installation
+
+5. Running the program
+
+6. Input and output files
+ 6.1. Summary of files
+ 6.2. The main input file
+ 6.2.1. General data
+ 6.2.2 Molecule and energy parameter data
+ 6.2.2.1. General information
+ 6.2.2.2. Sequence information
+ 6.2.2.3. Dihedral angle restraint information
+ 6.2.2.4. Disulfide-bridge data
+ 6.2.3. Energy-term weights and parameter files
+ 6.2.4. (M)REMD/Hamiltonian (M)REMD setting specification
+ 6.2.5. Information of files from which to read conformations
+ 6.2.6. Information of reference structure and comparing scheme
+ 6.3. The structure of the main output file (out)
+ 6.4. The thermodynamic quantity and ensemble average (stat) files
+ 6.5. The conformation summary with classification (stat) files
+ 6.6. The histogram files
+ 6.7. The rmsd-radius of gyration potential of mean force files
+ 6.8. The PDB files
+ 6.8. The compresses Cartesian coordinates (cx) file.
+
+7. 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. REFERENCES
+-------------
+
+[1] S. Kumar, D. Bouzida, R.H. Swendsen, P.A. Kollman, J.M. Rosenberg.
+ The weighted histogram analysis method for free-energy calculations
+ on biomolecules. I. The method.
+ J. Comput. Chem., 1992, 13, 1011-1021.
+
+[2] A. Liwo, M. Khalili, C. Czaplewski, S. Kalinowski, S. Oldziej, K. Wachucik,
+ H.A. Scheraga.
+ Modification and optimization of the united-residue (UNRES) potential
+ energy function for canonical simulations. I. Temperature dependence of the
+ effective energy function and tests of the optimization method with single
+ training proteins.
+ J. Phys. Chem. B, 2007, 111, 260-285.
+
+[3] S. Oldziej, A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
+ Optimization of the UNRES force field by hierarchical design of the
+ potential-energy landscape. 2. Off-lattice tests of the method with single
+ proteins. J. Phys. Chem. B., 2004, 108, 16934-16949.
+
+[4] S. Oldziej, A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
+ Optimization of the UNRES force field by hierarchical design of the
+ potential-energy landscape. 2. Off-lattice tests of the method with single
+ proteins. J. Phys. Chem. B., 2004, 108, 16934-16949.
+
+3. FUNCTIONS OF THE PROGRAM
+---------------------------
+
+The program processes the results of replica exchange (REMD) or multiplexed
+replica exchange molecular dynamics (MREMD) simulations with UNRES to compute
+the probabilities of the obtained conformations to occur at particular
+temperatures. The program is based on the variant of the weighted histogram
+analysis (WHAM) method [1] described in ref [2].
+
+The program outputs the following information:
+
+a) Temperature profiles of thermodynamic and structural ensemble-averaged
+ quantities.
+
+b) Histograms of native-likeness measure q (defined by eqs 8-11 of ref [2]).
+
+c) Optionally the most probable conformations at REMD temperatures.
+
+d) Optionally the coordinates with information to compute probabilities
+ for the conformations to occur at any temperature.
+
+The program takes usually UNRES compressed coordinate files (cx files) from
+MREMD obtained by using the TRAJ1FILE option. The user can request to
+partition the whole run into equal slices (or windows), each starting from,
+say, snapshot n (for each trajectory) and ending at snapshot n+1.
+Alternatively, the UNRES Cartesian coordinate (x files) can be input; however,
+they must contain only the analyzed portion of the trajectories; they
+are usually prepared from single trajectories by using xdrf2x.
+
+Two versions of the program are provided:
+
+a) Canonical version which treats single polypeptide chains; the source code
+is in WHAM/src directory.
+
+b) Version for oligomeric proteins; multiple chains are handled by inserting
+dummy residues in the sequence; the source code is in WHAM/src-M directory.
+
+4. INSTALLATION
+---------------
+
+Customize Makefile to your system. See section 7 of the description of UNRES
+for compiler flags that are used to created executables for a particular
+force field. There are already several Makefiles prepared for various systems
+and force fields.
+
+Run make in the WHAM/src directory WHAM/src-M directory for multichain
+version. Make sure that MPI is installed on your system; the present program
+runs only in parallel mode.
+
+5. RUNNING THE PROGRAM
+----------------------
+
+The program requires a parallel system to run. Depending on system,
+either the wham.csh C-shell script (in WHAM/bin directory) can be started
+using mpirun or the binary in the C-shell script must be executed through
+mpirun. See the wham.csh C-shell script and section 6 for the files
+processed by the program.
+
+6. INPUT AND OUTPUT FILES
+-------------------------
+
+6.1. SUMMARY OF THE FILES
+-------------------------
+
+The C-shell script wham.csh is used to run the program (see the WHAM/bin
+directory). The data files that the script needs are mostly the same as
+for UNRES (see section 6 of UNRES description). In addition, the environmental
+variable CONTFUN specifies the method to assess whether two side chains
+are at contact; if CONTFUN=GB, the criterion defined by eq 8 of ref 4 is
+used to assess whether two side chains are at contact. Also, the parameter
+files from the C-shell scripts are overridden if the data from Hamiltonian
+MREMD are processed; if so, the parameter files are defined in the main
+input file.
+
+The main input file must have inp extension. If it is INPUT.inp, the output
+files are as follows:
+
+INPUT.out_POTxxx - output files from different processors (INPUT.out_000 is the
+ main output file). POT is the identifier of the sidechain-sidechain
+ potential.
+
+INPUT_POT_GB_xxx.stat or INPUT_POT_slice_YYXXX.stat- the summary conformation-
+ classification file from processor xxx (each processor handles part of
+ conformations); the second occurs if the run is partitioned into slices.
+
+INPUT.thermal or INPUT_slice_yy.thermal - thermodynamic functions and
+ temperature profiles of the ensemble averages (the second form if the
+ run is partitioned into slices).
+
+INPUT_T_xxx.pdb or INPUT_slice_yy_T_xxx.pdb - top conformations the number
+ of these conformations is selected by the user) in PDB format.
+
+INPUT.cx - the compressed UNRES coordinate file with information to compute
+ the probability of a given conformation at any temperature.
+
+INPUT.hist INPUT_slice_xx.hist INPUT_par_yy.hist INPUT_par_yy_slice_zz.x
+ - histograms of q at MREMD temperatures.
+
+INPUT.ent INPUT_slice_xx.ent INPUT_par_yy.ent INPUT_par_yy_slice_xx.ent
+ - the histogram(s) of energy density.
+
+INPUT.rmsrgy INPUT_par_yy.rmsrgy INPUT_slice_xx.rmsrgy or
+ INPUT_par_yy_slice_xx.rmsrgy
+ - the 2D histogram(s) of rmsd from the experimental structure and radius
+ of gyration.
+
+6.2. MAIN INPUT FILE
+--------------------
+
+This file has the same structure as the UNRES input file; most of the data are
+input in a keyword-based form (see section 7.1 of UNRES description). The data
+are grouped into records, referred to as lines. Each record, except for the
+records that are input in non-keyword based form, can be continued by placing
+an ampersand (&) in column 80. Such a format is referred to as the data list
+format.
+
+In the following description, the default values are given in parentheses.
+
+6.2.1. General data (data list format)
+--------------------------------------
+
+N_ENE (N_ENE_MAX) - the number of energy components
+
+SYM (1) - number of chains with same sequence (for oligomeric proteins only),
+
+HAMIL_REP - if present, Hamiltonian process the results of replica exchange runs
+ (replicas with different parameters of the energy function)
+
+NPARMSET (1) - number of energy parameter sets (>1 only for Hamiltonian
+ replica exchange simulations)
+
+SEPARATE_PARSET - if present, HREMD was run in a mode such that only temperature
+ but not energy-function parameters was exchanged
+
+IPARMPRINT (1) - number of parameter set with which to construct conformational
+ ensembles; important only when HREMD runs are processed
+
+ENE_ONLY - if present, only conformational energies will be calculated and
+ printed; no WHAM iteration
+
+EINICHECK (2) - > 0 compare the conformational energies against those stored in
+ the coordinate file(s); 1: compare but print only a warning message if
+ different; 2: compare and terminate the program if different; 0: don't
+ compare.
+
+MAXIT (5000) - maximum number of iterations in solving WHAM equations
+
+ISAMPL (1) - input conformation sampling frequency (e.g., if ISAMPL=5, only
+ each 5th conformation will be read)
+
+NSLICE (1) - number of "slices" or "windows" into which each trajectory will
+ be partitioned; each slice will be analyzed independently
+
+FIMIN (0.001) - maximum average difference between window free energies
+ between the current and the previous iteration
+
+ENSEMBLES (0) - number of conformations (ranked according to probabilities) to
+ be output to PDB file at each MREMD temperature; 0 means that no
+ conformations will be output. Non-zero values should not be used when NSLICE>1
+
+CLASSIFY - if present, each conformation will be assigned a class, according
+to the scheme described in ref [3]
+
+DELTA (0.01) - one dimension bin size of the histogram in q
+
+DELTRMS (0.05) - rms dimension bin size in rms-radius of gyration histograms
+
+DELTRGY (0.05) - radius of gyration bin size in rms-radius of gyration histograms
+
+NQ (1) - number of q's (can be for entire molecule, fragments, and pairs of
+ fragments)
+
+CXFILE - produce the compressed coordinate file with information necessary to
+ compute the probabilities of conformations at any temperature
+
+HISTOUT - if present, the histograms of q at MREMD temperatures are
+ constructed and printed to main output file
+
+HISTFILE - if present, the histograms are also printed to separate files
+
+ENTFILE - if present, histogram of density of states (entropy) is constructed
+ and printed
+
+RMSRGYMAP - if present, 2D histograms of radius of rmsd and radius of gyration at MREMD
+ temperatures are constructed and printed
+
+WITH_DIHED_CONSTR - if present, dihedral-angle restraints were imposed in the
+ processed MREMD simulations
+
+RESCALE (1) - Choice of the type of temperature dependence of the force field.
+0 - no temperature dependence
+1 - homographic dependence (not implemented yet with any force field)
+2 - hyperbolic tangent dependence [18].
+
+6.2.2 Molecule and energy parameter data
+----------------------------------------
+
+6.2.2.1. General information
+----------------------------
+
+SCAL14 (0.4) - scale factor of backbone-electrostatic 1,4-interactions
+
+SCALSCP (1.0) - scale factor of SC-p interactions
+
+CUTOFF (7.0) - cut-off on backbone-electrostatic interactions to compute 4-
+ and higher-order correlations
+
+DELT_CORR (0.5) - thickness of the distance range in which the energy is
+decreased to zero
+
+ONE_LETTER - if present, the sequence is to be read in 1-letter code,
+ otherwise 3-letter code
+
+6.2.2.2. Sequence information
+-----------------------------
+
+1st record (keyword-based input):
+
+NRES - number of residues, including the UNRES dummy terminal residues, if present
+
+Next records: amino-acid sequence
+
+3-letter code: Sequence is input in format 20(1X,A3)
+
+1-letter code: Sequence is input in format 80A1
+
+6.2.2.3. Dihedral angle restraint information
+---------------------------------------------
+
+This is the information about dihedral-angle restraints, if any are present.
+It is specified only when WITH_DIHED_CONSTR is present in the first record.
+
+1st line: ndih_constr - number of restraints (free format)
+
+2nd line: ftors - force constant (free format)
+
+Each of the following ndih_constr lines:
+
+idih_constr(i),phi0(i),drange(i) (free format)
+
+idih_constr(i) - the number of the dihedral angle gamma corresponding to the
+ith restraint
+
+phi0(i) - center of dihedral-angle restraint
+
+drange(i) - range of flat well (no restraints for phi0(i) +/- drange(i))
+
+6.2.2.4. Disulfide-bridge data
+------------------------------
+
+1st line: NS, (ISS(I),I=1,NS) (free format)
+
+NS - number of cystine residues forming disulfide bridges
+
+ISS(I) - the number of the Ith disulfide-bonding cystine in the sequence
+
+2nd line: NSS, (IHPB(I),JHPB(I),I=1,NSS) (free format)
+
+NSS - number of disulfide bridges
+
+IHPB(I),JHPB(I) - the first and the second residue of ith disulfide link
+
+Because the input is in free format, each line can be split
+
+6.2.3. Energy-term weights and parameter files
+----------------------------------------------
+
+There are NPARMSET records specified below.
+
+All items described in this section are input in keyword-based mode.
+
+1st record: Weights for the following energy terms:
+
+WSC (1.0) - side-chain-side-chain interaction energy
+
+WSCP (1.0) - side chain-peptide group interaction energy
+
+WELEC (1.0) - peptide-group-peptide group interaction energy
+
+WEL_LOC (1.0)- third-order backbone-local correlation energy
+
+WCORR (1.0) - fourth-order backbone-local correlation energy
+
+WCORR5 (1.0) - fifth-order backbone-local correlation energy
+
+WCORR6 (1.0) - sixth-order backbone-local correlation energy
+
+WTURN3 (1.0) - third-order backbone-local correlation energy of pairs of
+ peptide groups separated by a single peptide group
+
+WTURN4 (1.0) - fourth-order backbone-local correlation energy of pairs of
+ peptide groups separated by two peptide groups
+
+WTURN6 (1.0) - sixth-order backbone-local correlation energy for pairs of
+ peptide groups separated by four peptide groups
+
+WBOND (1.0) - virtual-bond-stretching energy
+
+WANG (1.0) - virtual-bond-angle-bending energy
+
+WTOR (1.0) - virtual-bond-torsional energy
+
+WTORD (1.0) - virtual-bond-double-torsional energy
+
+WSCCOR (1.0) - sequence-specific virtual-bond-torsional energy
+
+WDIHC (0.0) - dihedral-angle-restraint energy
+
+WHPB (1.0) - distance-restraint energy
+
+2nd record: Parameter files. If filename is not specified that corresponds to
+particular parameters, the respective name from the C-shell script will be
+assigned. If no files are to be specified, an empty line must be inserted.
+
+BONDPAR - bond-stretching parameters
+
+THETPAR - backbone virtual-bond-angle-bending parameters
+
+ROTPAR - side-chain-rotamer parameters
+
+TORPAR - backbone-torsional parameters
+
+TORDPAR - backbone-double-torsional parameters
+
+FOURIER - backbone-local - backbone-electrostatic correlation parameters
+
+SCCORAR - sequence-specific backbone-torsional parameters (not used at
+ present)
+
+SIDEPAR - side-chain-side-chain-interaction parameters
+
+ELEPAR - backbone-electrostatic-interaction parameters
+
+SCPPAR - backbone-side-chain-interaction parameters
+
+6.2.4. (M)REMD/Hamiltonian (M)REMD setting specification
+--------------------------------------------------------
+
+If HAMIL_REP is present in general data, read the following group of records
+only once; otherwise, read for each parameter set (NPARSET times total)
+
+NT (1) - number of temperatures
+
+REPLICA - if present, replicas in temperatures were specified with this parameter set
+
+UMBRELLA - if present, umbrella-sampling was run with this parameter set
+
+READ_ISET - if present, umbrella-sampling-window number is read from the compressed Cartesian
+ coordinate (cx) file even if the data are not from umbrella-sampling run(s).
+ ISET is present in the cx files from the present version of UNRES.
+
+Following NT records are for consecutive temperature replicas; each record is
+organized as keyword-based input:
+
+TEMP (298.0) - initial temperature of this replica (replicas in MREMD)
+
+FI (0.0) - initial values of the dimensionless free energies for all q-restraint
+ windows for this replica (NR values)
+
+KH (100.0) - force constants of q restraints (NR values)
+
+Q0 (0.0d0) - q-restraint centers (NR values)
+
+6.2.5. Information of files from which to read conformations
+------------------------------------------------------------
+
+If HAMIL_REP is present in general data, read the following two records
+only once; otherwise, read for each parameter set (NPARSET times total)
+
+1st record (keyword-based input):
+
+For temperature replica only ONE record is read; for non-(M)REMD runs, NT
+records must be supplied. The records are in keyword-based format.
+
+NFILE_ASC - number of files in ASCII format (UNRES Cartesian coordinate (x)
+ files) for current parameter set
+
+NFILE_CX - number of compressed coordinate files (cx files) for current
+ parameter set.
+
+NFILE_BIN - number of binary coordinate files (now obsolete because it
+ requires initial conversion of ASCII format trajectories into binary format)
+
+It is strongly recommended to use cx files from (M)REMD runs with TRAJ1FILE
+option. Multitude of trajectory files which are opened and closed by different
+processors might impair file system accessibility. Should you wish to process
+trajectories each one of which is stored in a separate file, better collate
+the required slices of them first to an x file by using the xdrf2x program
+piped to the UNIX cat command.
+
+2nd record:
+
+coordinate file name(s) without extension
+
+6.2.6. Information of reference structure and comparing scheme
+-----------------------------------------------------------------
+
+The following records pertain to setting up the classification of conformation
+aimed ultimately at obtaining a class numbers. Fragments and pairs of
+fragments are specified and compared against those of reference structure in
+terms of secondary structure, number of contacts, rmsd, virtual-bond-valence
+and dihedral angles, etc. Then the class number is constructed as described in
+ref 3. A brief description of comparison procedure is as follows:
+
+1. Elementary fragments usually corresponding to elements of secondary
+or supersecondary structure are selected. Based on division into fragments,
+levels of structural hierarchy are defined.
+
+2. At level 1, each fragment is checked for agreement with the corresponding
+fragment in the native structure. Comparison is carried out at two levels:
+the secondary structure agreement and the contact-pattern agreement level.
+
+At the secondary structure level the secondary structure (helix, strand
+or undefined) in the fragment is compared with that in the native fragment
+in a residue-wise manner. Score 0 is assigned if the structure is different
+in more than 1/3 of the fragment, 1 is assigned otherwise.
+
+The contact-pattern agreement level compares the contacts between the peptide
+groups of the backbone of the fragment and the native fragment and also
+compares their virtual-bond dihedral angles gamma. It is allowed to shift
+the sequence by up to 3 residues to obtain contact pattern match. A score
+of 0 is assigned if more than 1/3 of native contacts do not occur or
+there is more than 60 deg (usually, but this cutoff can be changed) maximum
+difference in gamma. Otherwise score 1 is assigned.
+
+The total score of a fragment is an octal number consisting of bits
+hereafter referred to S (secondary structure) C (contact match) and H
+(sHift) (they are in the order HCS). Their values are as follows:
+
+S - 1 native secondary structure; 0 otherwise;
+C - 1 native contact pattern; 0 otherwise;
+H - 1 contact match obtained without sequence shift 0 otherwise.
+
+For example, octal 7 (111) corresponds to native secondary structure, native
+contact pattern, and no need to shift the sequence for contact match;
+octal 1 (001) corresponds to native secondary structure only (i.e., nonnative
+contact pattern).
+
+3. At level 2, contacts between (i) the peptide groups or (ii) the side chains
+within pairs of fragments are compared. Case (i) holds when we seek contacts
+between the strands of a larger beta-sheet formed by two fragments, case (ii)
+when we seek the interhelix or helix-beta sheet contacts. Additionally,
+the pairs of fragments are compared with their native counterparts by rmsd.
+Score 0 is assigned to a pair of fragments, if it has less than 2/3 native
+contacts and too large rmsd (a cut-off of 0.1 A/residue is set), score 1 if
+it has enough native contacts and sufficiently low rmsd, but the sequence
+has to be shifted to obtain a match, and score 2, if sufficient match is
+obtained without shift.
+
+4. At level 3 and higher, triads, quadruplets,..., etc. of fragments are
+compared in terms of rmsd from their native counterparts (the last level
+corresponds to comparing whole molecules). The score (0, 1, or 2) is assigned
+to each composite fragment as in the case of level 2.
+
+5. The TOTAL class number of a structure is a binary number composed of
+parts of scores of fragments, fragment pairs, etc. It is illustrated
+on the following example; it is assumed that the molecule has three fragment
+as in the case of 1igd.
+
+level 1 level 2 level 3
+123 123 123||1-2 1-3 2-3 1-2 1-3 2-3 || 1-2-3 | 1-2-3 ||
+sss|ccc|hhh|| c c c | h h h || r | h ||
+
+Bits s, c, and h of level 1 are explained in point 2; bits c and h of level
+2 pertain to contact-pattern match and shift; bits r and h of level 3 pertain
+to rmsd match and shift for level 3.
+
+The input is specified as follows:
+
+
+Program to classify structures
+
+1st record (keyword-based input):
+
+VERBOSE : if present, detailed output in classification (use if you want to
+ fill up the disk)
+
+PDBREF : if present, the reference structure is read from the pdb
+
+BINARY : if present, the class will be output in octal/quaternary/binary format
+ for levels 1, 2, and 3, respectively
+
+DONT_MERGE_HELICES : if present, the pieces of helices that contain only
+ small breaks of hydrogen-bonding contacts (e.g., a kink) are not merged
+ in a larger helix
+
+NLEVEL=n : number of classification levels
+
+n>0 - the fragments for n levels will be defined manually
+n<0 - the number of levels is -n and the fragments will be detected automatically
+
+START=n : the number of conformation at which to start
+
+END=n : the number of conformation at which to end
+
+FREQ=n (1) : sampling frequency of conformations; e.g. FREQ=2 means that every
+ second conformation will be considered
+
+CUTOFF_UP=x : upper boundary of rmsd cutoff (the value is per 50 residues)
+
+CUTOFF_LOW=x : lower boundary of rmsd cutoff (per 50 residues)
+
+RMSUP_LIM=x : lower absolute boundary of rmsd cutoff (regardless of fragment
+ length)
+
+RMSUPUP_LIM=x : upper absolute boundary of rmsd cutoff (regardless of fragment
+ length)
+
+FRAC_SEC=x (0.66666) the fraction of native secondary structure
+ to consider a fragment native in secondary structure
+
+2nd record:
+
+For nlevel < 0 (automatic fragment assignment):
+
+SPLIT_BET=n (0) : if 1, the hairpins are split into strands and strands are
+ considered elementary fragments
+
+ANGCUT_HEL=x (50): cutoff on gamma angle differences from the native for a helical
+ fragment
+
+MAXANG_HEL=x (60) : as above but maximum cutoff
+
+ANGCUT_BET=x (90), MAXANG_BET=x (360), ANGCUT_STRAND=xi (90), MAXANG_STRAND=x (360)
+ same but for a hairpin or sheet fragment.
+
+FRAC_MIN=x (0.6666) : minimum fraction of native secondary structure
+
+NC_FRAC_HEL=x (0.5) : fraction of native contacts for a helical fragment
+
+NC_REQ_HEL=x (0) : minimum required number of contacts
+
+NC_FRAC_BET=x (0.5), NC_REQ_BET=x (0) : same for beta sheet fragments
+
+NC_FRAC_PAIR=x (0.3), NC_REQ_PAIR=x (0) : same for pairs of segments
+
+NSHIFT_HEL=n (3), NSHIFT_BET=n (3), NSHIFT_STRAND=n (3), NSHIFT_PAIR=n (3) :
+ allowed sequence shift to match native and compared structure for the
+ respective types of secondary structure
+
+RMS_SINGLE=n (0), CONT_SINGLE=n (1), LOCAL_SINGLE=n (1), RMS_PAIR=n (0),
+
+CONT_PAIR=n (1) : types of criteria in considering the geometry of a fragment
+ or pair native; 1 means that the criterion is turned on
+
+For nlevel > 0 (manual assignment):
+
+Level 1:
+
+1st line:
+
+NFRAG=n : number of elementary fragments
+
+Next lines (one group of lines per each fragment):
+
+1st line:
+
+NPIECE=n : number of segments constituting the fragment
+
+ANGCUT, MAXANG, FRAC_MIN, NC_FRAC, NC_REQ : criterial numbers of native-likeness
+ as for automatic classification
+
+LOCAL, ELCONT, SCCONT, RMS : types of criteria implemented, as for automatic
+ classification except that ELECONT and SCCONT mean that electrostatic or
+ side-chain contacts are considered, respectively
+
+NPIECE following lines:
+
+IFRAG1=n, IFRAG2=n : the start and end residue of a continuous segment constituting
+ a fragment
+
+Level 2 and higher:
+
+1st line:
+
+NFRAG=n : number of fragments considered at this level
+
+For each fragment the following line is read:
+
+NPIECE=n : number of elementary fragments (as defined at level 1) constituting this
+ composite fragment
+
+IPIECE=i1 i2 ... in: the numbers of these fragments
+
+NC_FRAC, NC_REQ : contact criteria (valid only for level 2)
+
+ELCONT, SCCONT, RMS : as for level 1; note, that for level 3 and higher the only
+ criterion of nativelikeness is rms
+
+3rd (for nlevel<0) or following (for n>0) line:
+
+Name of the file with reference structure (e.g., the pdb file with the
+ experimental structure)
+
+6.3. The structure of the main output file (out)
+------------------------------------------------
+
+The initial portion of the main output file, named INPUT.out_POT_000
+contains information of parameter files specified in the C-shell script,
+compilation info, and the UNRES numeric code of the amino-acid sequence.
+Subsequently, actual energy-term weights and parameter files are printed.
+If lprint was set at .true. in parmread.F, all energy-function
+parameters are printed. If REFSTR was specified in the control-data list,
+the program then outputs the read reference-structure coordinates and
+partition of structure into fragments.
+
+Subsequently, the information about the number of structures read in and
+those that were rejected is printed followed by succinct information form
+the iteration process. Finally, the histograms (also output separately to
+specific histogram files; see section 6.6) and the data of the dependence of
+free energy, energy, heat capacity, and conformational averages on temperature
+are printed (these are also output separately to file described in section
+6.6).
+
+The output files corresponding to non-master processors
+(INPUT.out_POT_xxx where xxx>0 contain only the information up to the
+iteration protocol. These files can be deleted right after the run.
+
+6.4. The thermodynamic quantity and ensemble average (thermal) files
+-----------------------------------------------------------------
+
+The files INPUT.thermal or INPUT_slice_yy.thermal contain thermodynamic,
+ensemble-averaged conformation-dependent quantities and their temperature
+derivatives. The structure of a record is as follows:
+
+ T F E q_1...q_n rmsd Rgy Cv var(q_1)...var(q_n) var(rmsd) var(Rgy) cov(q_1,E)...cov(q_n,E) cov(rmsd,E) cov(Rgy,E)
+ 298.0 -83.91454 -305.28112 0.30647 6.28347 11.61204 0.70886E+01 0.35393E-02 0.51539E+01 0.57012E+00 0.43802E+00 0.62384E+01 0.33912E+01
+
+where:
+
+T: absolute temperature (in K),
+
+F: free energy at T,
+
+E: average energy at T,
+
+q_1..q_n: ensemble-averaged q values at T (usually only the total q corresponding to whole
+ molecule is requested, as in the example above, but the user can specify
+ more than one fragment or pair of fragments for which the q's are
+ calculated, If there's no reference structure, this entry contains
+ a 0,
+
+rmsd: ensemble-averaged root mean square deviation at T,
+
+Rgy: ensemble-averaged radius of gyration computed from Calpha coordinates at T,
+
+Cv: heat capacity at T,
+
+var(q_1)...var(q_n): variances of q's at T,
+
+var(rmsd): variance of rmsd at T,
+
+var(Rgy): variance of radius of gyration at T,
+
+cov(q_1,E)...cov(q_n,E): covariances of q's and energy at T,
+
+cov(rmsd,E): covariance of rmsd and energy at T,
+
+cov(Rgy,E): covariance of radius of gyration and energy at T.
+
+According to Camacho and Thirumalali (Europhys. Lett., 35, 627, 1996), the
+maximum of the variance of the radius of gyration corresponds to the collapse
+point of a polypeptide chain and the maximum variance of q or rmsd corresponds to
+the midpoint of the transition to the native structure. More precisely, these
+points are inflection points in the plots of the respective quantities which,
+with temperature-independent force field, are proportional to their covariances
+with energy.
+
+6.5. The conformation summary with classification (stat) files
+--------------------------------------------------------------
+
+The stat files (with names INPUT_POT_xxx.stat or
+INPUT_POT_sliceyyxxx.stat; where yy is the number of a slice and xxx
+is the rank of a processor) contain the output of the classification
+of subsequent conformations (equally partitioned between processors). The
+files can be concatenated by processor rank to get a summary file. Each line
+has the following structure (example values are also provided):
+
+ | level 1 | level 2 | level3 |
+ | | | |
+ whole mol | frag1 frag2 frag3 cl1 | level3 | |
+No energy rmsd q ang dif|n1n2 n3 rms q ang rms q ang rms q ang | nc1nc2 rms q rms q cl2| rms cl3|class
+ 9999 -122.42 4.285 0.3751 47.8 |4 10 21 0.6 0.33 16.7 3.6 0.42 56.3 0.7 0.12 16.5 737 | 9 0 1.6 0.20 4.3 0.20 20 | 0 4.0 2 |737.20.2
+
+No - number of conformation
+
+whole mol denotes the characteristics of the whole molecule
+q - 1-(Wolynes' q)
+
+level 1, 2, and 3 denote the characteristics computed for the respective fragments
+as these levels.
+
+n1, n2, n3 - number of native contacts for a given segment
+
+cl1, cl2, cl3 - group of segment classes for segments at level 1, 2, and 3, respectively
+
+class - total class of the conformation
+
+The octal/quaternary/binary numbers denoting the class for a fragment at level 1, 2,
+and 3, respectively, are described in ref. 3
+
+6.6. The histogram files
+------------------------
+
+The histogram file with names INPUT_[par_yy][_slice_xx].hist where xx denotes
+the number of the slice and yy denotes the number of the parameter if
+SEPARATE_PARSET was specified in input contain histograms of q at replica
+temperatures and energy-parameter sets; with SEPARATE_PARSET histograms
+corresponding to subsequent parameter sets are saved in files with par_yy
+infixes. The histograms are multidimensional if q is a vector (usually,
+however, q corresponds to the entire molecule and, consequently, the
+histograms are one-dimensional). The histogram files are printed if histfile
+and histout was specified in the control data record.
+
+Each line of a histogram file corresponds to a given (multidimensional) bin in
+q contains the following:
+
+q_1,...,q_n at a given bin (format f6.3 for each)
+
+histogram values for subsequent replica temperatures (format e20.10 for each)
+
+iparm (the number of parameter set; format i5)
+
+If SEPARATE_PARSET was not specified, the entries corresponding to each
+parameter follow one another.
+
+The state density (microcanonical entropy) is printed to file(s)
+INPUT[_slice_xx].ent. Each line contains the left boundary of the energy
+bin and ln(state density) followed by " ent" string. At present, the state
+density is calculated correctly only if one energy-parameter set is used.
+
+6.7. The rmsd-radius of gyration potential of mean force files
+------------------------------------------
+
+These files with names INPUT[_par_yy][_slice_xx].rmsrgy contain the
+two-dimensional potentials of mean force in rmsd and radius of gyration
+at all replica-exchange temperatures and for all energy-parameter sets.
+A line contains the left boundaries of the radius of gyration - rmsd bin
+(radius of gyration first) (format 2f8.2) and the PMF values at all
+replica-exchange temperatures (e14.5), followed by the number of the parameter
+set. With SEPARATE_PARSET, the PMFs corresponding to different parameter sets
+are printed to separate files.
+
+6.8. The PDB files
+------------------
+
+The PDB files with names INPUT_[slice_xx_]Tyyy.pdb, where Tyyy specifies
+a given replica temperature contain the conformations whose probabilities at
+replica temperature T sum to 0.99, after sorting the conformations by
+probabilities in descending order. The PDB files follow the standard format;
+see ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf.
+For single-chain proteins, an example is as follows:
+
+REMARK CONF 9059 TEMPERATURE 330.0 RMS 8.86
+REMARK DIMENSIONLESS FREE ENERGY -1.12726E+02
+REMARK ENERGY -2.22574E+01 ENTROPY -7.87818E+01
+ATOM 1 CA VAL 1 8.480 5.714 -34.044
+ATOM 2 CB VAL 1 9.803 5.201 -33.968
+ATOM 3 CA ASP 2 8.284 2.028 -34.925
+ATOM 4 CB ASP 2 7.460 0.983 -33.832
+.
+.
+.
+ATOM 115 CA LYS 58 28.446 -3.448 -12.936
+ATOM 116 CB LYS 58 26.613 -4.175 -14.514
+TER
+CONECT 1 3 2
+.
+.
+.
+CONECT 113 115 114
+CONECT 115 116
+
+where
+
+CONF is the number of the conformation from the processed slice of MREMD
+trajectories
+
+TEMPERATURE is the replica temperature
+
+RMS is the Calpha rmsd from the reference (experimental) structure.
+
+DIMENSIONLESS FREE ENERGY is -log(probability) (equation 14 of ref 2)
+for the conformation at this replica temperature calculated by WHAM.
+
+ENERGY is the UNRES energy of the conformation at the replica temperature
+(note that UNRES energy is in general temperature dependent).
+
+ENTROPY is the omega of equation 15 of ref 2 of the conformation
+
+In the ATOM entries, CA denotes a Calpha atom and CB denotes UNRES side-chain
+atom. The CONECT entries specify the Calpha(i)-Calpha(i-1),
+Calpha(i)-Calpha(i+1) and Calpha(i)-SC(i) links.
+
+The PDB files generated for oligomeric proteins are similar except that
+chains are separated with TER and molecules with ENDMDL records and chain
+identifiers are included. An example is as follows:
+
+REMARK CONF 765 TEMPERATURE 301.0 RMS 11.89
+REMARK DIMENSIONLESS FREE ENERGY -4.48514E+02
+REMARK ENERGY -3.58633E+02 ENTROPY 1.51120E+02
+ATOM 1 CA GLY A 1 -0.736 11.305 24.600
+ATOM 2 CA TYR A 2 -3.184 9.928 21.998
+ATOM 3 CB TYR A 2 -1.474 10.815 20.433
+.
+.
+.
+ATOM 40 CB MET A 21 -4.033 -2.913 27.189
+ATOM 41 CA GLY A 22 -5.795 -10.240 27.249
+TER
+ATOM 42 CA GLY B 1 6.750 -6.905 19.263
+ATOM 43 CA TYR B 2 5.667 -4.681 16.362
+.
+.
+.
+ATOM 163 CB MET D 21 4.439 12.326 -4.950
+ATOM 164 CA GLY D 22 10.096 14.370 -9.301
+TER
+CONECT 1 2
+CONECT 2 4 3
+.
+.
+.
+CONECT 39 41 40
+CONECT 42 43
+.
+.
+.
+CONECT 162 164 163
+ENDMDL
+
+6.8. The compressed Cartesian coordinates (cx) files
+----------------------------------------------------
+
+These files contain compressed data in the Europort Data Compression XDRF
+library format written by Dr. F. van Hoesel, Groeningen University
+(http://hpcv100.rc.rug.nl/xdrfman.html). The files are written
+by the cxwrite subroutine. The resulting cx file contains the omega
+factors to compute probabilities of conformations at any temperature
+and any energy-function parameters if Hamiltonian replica exchange was
+performed in the preceding UNRES run. The files have general names
+INPUT[_par_yy][_slice_xx].cx where xx is slice number and yy is parameter-set
+number.
+
+The items written to the cx file are as follows (the precision is 5
+significant digits):
+
+1) Cartesian coordinates of Calpha and SC sites
+2) nss (number of disulfide bonds)
+3) if nss > 0:
+ a) ihpb (first residue of a disulfide link)
+ b) jhpb (second residue of a disulfide link)
+4) UNRES energy at that replica temperature that the conformation was at
+ snapshot-recording time,
+5) ln(omega) of eq 15 of ref 2,
+6) Calpha rmsd
+7) conformation class number (0 if CLASSIFY was not specified).
+
+7. 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, 02/19/12
projects / unres.git / blobdiff