+++ /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