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.
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.
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).
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,ENER,NSS,(IHPB(I),JHPB(I),I=1,NSS)
(I5,F12.5,I2,9(1X,2I3))
(THETA(I),I=3,NRES)
(8F10.4)
The virtual-bond angles THETA (in degrees)
(PHI(I),I=4,NRES)
(8F10.4)
The virtual-bond dihedral angles GAMMA (in degrees)
(ALPH(I),I=2,NRES-1)
(OMEG(I),I=2,NRES-1)
(8F10.4)
The polar angles ALPHA and BETA of the side-chain centers (in degrees).
(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)
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)
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.
(Subroutine PDBOUT.)
These files are written in PDB standard (see. e.g., ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions). 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.
See the description of mol2 format (e.g., http://tripos.com/data/support/mol2.pdfhttp://tripos.com/data/support/mol2.pdf. Similar remarks apply as for the PDB format (section 2.2.4).
Each line of the stat file generated by MD/MREMD runs contains the following items in sequence:
For an USAMPL run, the following items follow the above list:
If PRINT_COMPON has been specified, the energy components are printed after the items described above.
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:
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:
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).
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.
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 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 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 |
where:
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 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 |
where
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 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 ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions. 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
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 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
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.htmlhttp://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 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):
The file with name file_clust.int 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 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 are in standard format (see ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdfftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions). 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.
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 CLUSTER 1 FREE ENERGY -7.65228E+01 AVE RMSD 8.22 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 TER CONECT 1 3 2 CONECT 3 5 4 . . CONECT 113 114 CONECT 115 116 TER 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 TER CONECT 1 3 2 CONECT 3 5 4 CONECT 113 114 CONECT 115 116 TER
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.
REMAR AVERAGE CONFORMATIONS AT TEMPERATURE 300.00 REMARK CLUSTER 1 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 TER CONECT 1 3 2 CONECT 3 5 4 . . . CONECT 76 78 77 CONECT 78 79 CONECT 79 80 CONECT 81 82 TER 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 TER CONECT 1 3 2 CONECT 3 5 4 . . . CONECT 76 78 77 CONECT 78 79 CONECT 79 80 CONECT 81 82 TER
Prepared by Adam Liwo, 04/10/18