X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=doc%2FWHAM.TXT;fp=doc%2FWHAM.TXT;h=0000000000000000000000000000000000000000;hp=44074337020018eea4b9172d765725c1e3c3db5c;hb=7e75cfee188bb6255d455c46c87b9f34cf46aa00;hpb=e62983fb4a02b190d8fbfda27a26ec7ce96799d8 diff --git a/doc/WHAM.TXT b/doc/WHAM.TXT deleted file mode 100644 index 4407433..0000000 --- a/doc/WHAM.TXT +++ /dev/null @@ -1,959 +0,0 @@ - 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