The output files produced by the UNRES server are those from UNRES and, if MREMD calculations were requested, also from WHAM and CLUSTER and the final all-atom model files. The file names begin with file_ for UNRES, WHAM, and cluster, while the files with the final all-atom models are model01.pdb - model05.pdb. It should be noted that only the files correspoding to the calculation types available when using the UNRES server are described in this document and that, for non-server UNRES jobs, other filename prefixes than file_ can be set; for details please see the UNRES web page.

The output from the UNRES-Dock is the same as from the regular MREMD simulation. The DockQ is used to measure quality of 5 docked models.


The main output file(s)

UNRES ``main'' output files (file.out_${POT}[processor], where, by defalut, ${POT} = GB, the Gay-Berne-type sidechain-sidechain interaction potential) are log files from a run. They contain the information of the molecule, force field, calculation type, control parameters, etc.; however, not the structures produced during the run or their energies except single-point energy evaluation and minimization-related runs.

Coordinate files

The structural information is included in coordinate files (*.int, *.x, *.pdb, *.mol2, *.cx) and statistics files (*.stat), respectively; these files are further processed by WHAM and CLUSTER or can be viewed by molecular viewers (pdb or mol2 files).

The internal coordinate (INT) file

This file contains the internal coordinates of the conformations produced by UNRES in non-MD runs. The virtual-bond lengths are assumed constant so only the angular variables are provided.


IT - the number of the conformation.
ENER - total energy.
NSS - the number of disulfide bridges.
(IHPB(I),JHPB(I),I=1,NSS) - the positions of the pairs of half-cystines . forming the bridges. If NSS > 9, the remaining pairs are written in the following lines in the (3X,11(1X,2I3)) format.


The virtual-bond angles THETA (in degrees)


The virtual-bond dihedral angles GAMMA (in degrees)


The polar angles ALPHA and BETA of the side-chain centers (in degrees).

The plain Cartesian coordinate (X) files

(Subroutine CARTOUT.)

This file contains the Cartesian coordinates of the α-carbon and side-chain-center coordinates. All conformations from an MD/MREMD trajectory are collated to a single file. The structure of each conformation's record is as follows:

1st line: time, potE, uconst, t_bath,nss, (ihpb(j), jhpb(j), j=1,nss), nrestr, (qfrag(i), i=1,nfrag), (qpair(i), i=1,npair), (utheta(i), ugamma(i), uscdiff(i), i=1,nfrag_back)

time: MD time (in ``molecular time units'' 1 mtu = 48.9 fs),
potE: potential energy,
uconst: restraint energy corresponding to restraints on Q and backbone geometry,
t_bath: thermostat temperature,
nss: number of disulfide bonds,
ihpb(j), jhpb(j): the numbers of linked cystines for jth disulfide bond,
nrestr: number of restraints on q and local geometry,
qfrag(i): q value for ith fragment,
qpair(i): q value for ith pair,
utheta(i): sum of squares of the differences between the theta angles of the current conformation from those of the experimental conformation,
ugamma(i): sum of squares of the differences beaten the gamma angles of the current conformation from those of the experimental conformation,
uscdiff(i): sum of squares of the differences between the Cartesian difference of the unit vector of the Cα -SC axis of the current conformation from those of the experimental conformation.

Next lines: Cartesian coordinates of the Cα atoms (including dummy atoms) (sequentially, 10 coordinates per line) Next lines: Cartesian coordinates of the SC atoms (including glycines and dummy atoms) (sequentially, 10 coordinates per line)

The compressed Cartesian coordinate (CX) files

These files are compressed binary files (extension cx). For each conformation, the items are written in the same order as specified in section 2.2.3. For MREMD runs, if TRAJ1FILE is specified on MREMD record, snapshots from all trajectories are written every time the coordinates are dumped. Thus, the file contains snapshot 1 from trajectory 1, ..., snapshot 1 from trajectory M, snapshot 2 from trajectory 1, ..., etc.

The compressed cx files can be converted to pdb file by using the xdrf2pdb auxiliary program (single trajectory files) or xdrf2pdb-m program (multiple trajectory files from MREMD runs generated by using the TRAJ1FILE option). The multiple-trajectory cx files are also input files for the auxiliary WHAM program.

The Brookhaven Protein Data Bank format (PDB) files

(Subroutine PDBOUT.)

These files are written in PDB standard (see. e.g., The REMARK, ATOM, SSBOND, HELIX, SHEET, CONECT, TER, and ENDMDL are used. The Cα (marked CA) and SC (marked CB) coordinates are output. The CONECT records specify the Cα - Cα and Cα - SC virtual bonds. Secondary structure is detected based on peptide-group contacts, as specified in ref 12. Dummy residues are omitted from the output. If the program has multiple-chain function, the presence of a dummy residue in a sequence starts a new chain, which is assigned the next alphabet letter as ID, and residue numbering is started over.

The SYBYLL (MOL2) files

See the description of mol2 format (e.g., Similar remarks apply as for the PDB format (section 2.2.4).

The summary (STAT) file

Each line of the stat file generated by MD/MREMD runs contains the following items in sequence:

step - the number of the MD step
time - time [unit is MTU (molecular time unit) equal to 48.9 fs]
Ekin - kinetic energy [kcal/mol]
Epot - potential energy [kcal/mol]
Etot - total energy (Ekin+Epot)
H-H0 - the difference between the cureent and initial extended Hamiltionian in Nose-Hoover or Nose-Poincare runs; not present for other thermostats.
RMSD - root mean square deviation from the reference structure (only in REFSTR has been specified) itemdamax - maximum change of acceleration between two MD steps
fracn - fraction of native side-chain concacts (very crude, based on SC-SC distance only)
fracnn - fraction of non-native side-chain contacts
co - contact order
temp - actual temperature [K]
T0 - initial (microcanonical runs) or thermostat (other run types) temperature [K]
Rgyr - radius of gyration based on Cα coordinates [A]
proc - in MREMD runs the number of the processor (the number of the trajectory less 1); not present for other runs.

For an USAMPL run, the following items follow the above list:

iset - the number of the restraint set
uconst - restraint energy pertaining to q-values
uconst_back - restraint energy pertaining to virtual-backbone restraints
(qfrag(i),i=1,nfrag) - q values of the specified fragments
(qpair(ii2),ii2=1,npair) - q values of the specified pairs of fragments
(utheta(i),ugamma(i),uscdiff(i),i=1,nfrag_back) - virtual-backbone and side-chain-rotamer restraint energies of the fragments specified

If PRINT_COMPON has been specified, the energy components are printed after the items described above.


Summary of the files

file.out_POTxxx - output files from different processors (file.out_000 is the main output file). POT is the identifier of the sidechain-sidechain potential.

file_POT_GB_xxx.stat or file_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.

file.thermal or file_slice_yy.thermal - thermodynamic functions and temperature profiles of the ensemble averages (the second form if the run is partitioned into slices).

file_T_xxx.pdb or file_slice_yy_T_xxx.pdb - top conformations the number of these conformations is selected by the user) in PDB format. - the compressed UNRES coordinate file with information to compute the probability of a given conformation at any temperature.

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 structure of the main output file

The initial portion of the main output file, named file.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 3.5).

The output files corresponding to non-master processors (file.out_POT_xxx where xxx > 0 contain only the information up to the iteration protocol. These files can be deleted right after the run.

The thermodynamic quantity and ensemble average (thermal) files

The files file.thermal or file_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
298.0 -83.91454 -305.28112 0.30647 6.28347 11.61204 0.70886E+01

var(q1) ... var(rmsd) var(Rgy) cov(q1,E) ... cov(rmsd,E) cov(Rgy,E)
var(qn)     cov(qn,E)    
0.35393E-02 0.51539E+01 0.57012E+00 0.43802E+00 0.62384E+01 0.33912E+01


T - absolute temperature (in K),

F - free energy at T,

E - average energy at T,

q1..qn : 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 is 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(q1)...var(qn) - variances of q's at T,

var(rmsd) - variance of rmsd at T,

var(Rgy) - variance of radius of gyration at T,

cov(q1,E)...cov(qn,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.

The conformation summary with classification (stat) files

The stat files (with names file_POT_xxx.stat or file_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):

    whole molecule
No energy rmsd q ang
9999 -122.42 4.285 0.3751 47.8

level 1
frag 1 frag 2 frag 3 class 1
n1 n2 n3 rmsd q ang rmsd q ang rmsd q ang  
4 10 21 0.6 0.33 16.7 3.6 0.42 56.3 0.7 0.12 16.5 737

level 2 level 3  
nc1 nc2 rmsd q rmsd q class 2 rmsd q class 3 class
9 0 1.6 0.20 4.3 0.20 20 0 4.0 2 737.20.2


No - the number of the conformation.

``whole molecule'' 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 (Oldziej et al., J. Phys. Chem. B., 2004, 108, 16934-16949).

The PDB files

The PDB files with names file_[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 For single-chain proteins, an example is as follows:

REMARK CONF    9059 TEMPERATURE  330.0 RMS   8.86
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
CONECT    1    3    2
CONECT  113  115  114
CONECT  115  116


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 C α i ... C α i-1 , C α i ... C α i+1 and C α 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 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
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
CONECT    1    2
CONECT    2    4    3
CONECT   39   41   40
CONECT   42   43
CONECT  162  164  163

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 ( 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 file[_par_yy][_slice_xx].cx where xx is slice number and yy is parameter-set.

The items written to the cx file are as follows (the precision is 5 significant digits):

  1. Cartesian coordinates of Calpha and SC sites</p>
  2. nss (number of disulfide bonds)
  3. if nss>0:
    1. ihpb (first residue of a disulfide link)
    2. jhpb (second residue of a disulfide link)
    3. UNRES energy at that replica temperature that the conformation was at snapshot-recording time,
    4. ln(omega) of eq 15 of (Liwo et al., J. Phys. Chem. B, 2007, 111, 260-285),
  4. Cα rmsd
  5. conformation class number (0 if CLASSIFY was not specified).


Summary of files

file_clust.out (single-processor mode) or file_clust.out_xxx (parallel mode) - output file(s) (file.out_000 is the main output file for parallel mode). - leading (lowest-energy) members of the families. in internal-coordinate format.
file_clust.x - leading members of the families in UNRES Cartesian coordinate format.
file_xxxx.pdb or file_xxxx_yyy.pdb (CLUST-UNRES) - PDB file of member yyy of family xxxx; yyy is omitted if the family contains only one member within a given energy cut-off.
file_TxxxK_yyyy.pdb - concatenated conformations in PDB format of the members of family yyyy clustered at T=xxxK ranked by probabilities in descending order at this temperature (CLUST-WHAM).
file_T_xxxK_ave.pdb - cluster-averaged coordinates and coordinates of a member of each family that is closest to the cluster average in PDB format, concatenated in a single file (CLUST-WHAM).

file_clust.tex - PicTeX code of the cluster tree (effectively obsolete).

file.rms - rmsds between conformations.

Output coordinate files

The internal coordinate (int) files

The file with name contains the angles theta, gamma, alpha, and beta of all residues of the leaders (lowest UNRES energy conformations from consecutive families for CLUST-UNRES runs and lowest free energy conformations for CLUST-WHAM runs). The format is the same as that of the file output by UNRES; see section 9.1.1 of UNRES description.

For CLUST-WHAM runs, the first line contains more items:

number of family (format i5)
UNRES free energy of the conformation (format f12.3)
Free energy of the entire family (format f12.3)
number of disulfide bonds (format i2)
list disulfide-bonded pairs (format 2i3)
conformation class number (0 if not provided) (format i10)

The Cartesian coordinate (x) files

The file with name file_clust.x contains the Cartesian coordinates of the alpha-carbon and side-chain-center coordinates. The coordinate format is as in section 9.1.2 of UNRES description and the first line contains the following items:

Number of the family (format I5)
UNRES free energy of the conformation (format f12.3)
Free energy of the entire family (format f12.3)
number of disulfide bonds (format i2)
list disulfide-bonded pairs (format 2i3)
conformation class number (0 if not provided) (format i10)

The PDB files

The PDB files are in standard format (see The ATOM records contain Calpha coordinates (CA) or UNRES side-chain-center coordinates (CB). For oligomeric proteins chain identifiers are present (A, B, ..., etc.) and each chain ends with a TER record. Coordinates of a single conformation or multiple conformations The header (REMARK) records and the contents depends on cluster run type. The next subsections are devoted to different run types.

The program generates a file for each family of conformations and a summary file with ensemble-averaged conformations for all families. These are described in the two next sections.

Conformation family files

For each family, the file name is file_TxxxK_yyyy.pdb, where yyyy is the number of the family and xxx is the integer part of the temperature (K). The first REMARK line in the file contains the information about the free energy and average rmsd of the entire cluster and, for each conformation, the initial REMARK line contains these quantities for this conformation. Same applies to oligomeric proteins, for which the TER records separate the chains and the ENDMDL record separates conformations. An example is given below.

REMARK 1BDD L18G full clust ENERGY    -7.33241E+01 RMS  10.40
ATOM      1  CA  VAL     1      18.059 -33.585   4.616  1.00  5.00
ATOM      2  CB  VAL     1      18.720 -32.797   3.592  1.00  5.00
ATOM    115  CA  LYS    58      29.641 -44.596  -8.159  1.00  5.00
ATOM    116  CB  LYS    58      27.593 -45.927  -8.930  1.00  5.00
CONECT    1    3    2
CONECT    3    5    4
CONECT  113  114
CONECT  115  116
REMARK 1BDD L18G full clust ENERGY    -7.33240E+01 RMS  10.04
ATOM      1  CA  VAL     1       3.174   2.833 -34.386  1.00  5.00
ATOM      2  CB  VAL     1       3.887   2.811 -33.168  1.00  5.00
ATOM    115  CA  LYS    58      16.682   6.695 -20.438  1.00  5.00
ATOM    116  CB  LYS    58      18.925   5.540 -20.776  1.00  5.00
CONECT    1    3    2
CONECT    3    5    4
CONECT  113  114
CONECT  115  116

Average-structure file

The file name is file_T_xxxK_ave.pdb. The entries are in pairs; the first one is cluster-averaged conformation and the second is a family member which has the lowest rmsd from this average conformation. Computing average conformations is explained in section 2.5 of ref 3. Example excerpts from an entry corresponding to a given family are shown below.

REMARK 2HEP clustering 300K ENERGY    -8.22572E+01 RMS   3.29
ATOM      1  CA  MET     1     -17.748  48.148 -19.284  1.00  5.96
ATOM      2  CB  MET     1     -17.373  47.911 -19.294  1.00  6.34
ATOM      3  CA  ILE     2     -18.770  49.138 -18.133  1.00  3.98
ATOM     80  CB  PHE    41     -14.353  44.680 -15.642  1.00  2.62
ATOM     81  CA  ARG    42     -11.619  41.645 -13.117  1.00  4.06
ATOM     82  CB  ARG    42     -11.330  40.378 -13.313  1.00  5.19
CONECT    1    3    2
CONECT    3    5    4
CONECT   76   78   77
CONECT   78   79
CONECT   79   80
CONECT   81   82
REMARK 2HEP clustering 300K ENERGY    -8.22572E+01 RMS   3.29
ATOM      1  CA  MET     1     -37.698  40.489 -32.408  1.00  5.96
ATOM      2  CB  MET     1     -38.477  39.426 -34.159  1.00  6.34
ATOM     80  CB  PHE    41     -35.345  50.342 -31.371  1.00  2.62
ATOM     81  CA  ARG    42     -33.603  54.332 -27.130  1.00  4.06
ATOM     82  CB  ARG    42     -33.832  53.074 -24.415  1.00  5.19
CONECT    1    3    2
CONECT    3    5    4
CONECT   76   78   77
CONECT   78   79
CONECT   79   80
CONECT   81   82

Prepared by Adam Liwo, 04/10/18