YASARA Molecular Dynamics Trajectory Analysis for 4mbs

1. About the simulation

The trajectory /home/kornel/big/mdanalysis/4mbs/4mbs has been analyzed with YASARA version 18.1.1.L.64 over a period of 1000.00 nanoseconds with 401 snapshots and the AMBER14 force field.

All plots and pictures in this report [like the simulated system below] are 1024 pixels wide, you can change the figurewidth variable in this macro as needed.

Figure-1: A ray-traced picture of the simulated system. The simulation cell boundary is set to periodic. Atoms that stick out of the simulation cell will be wrapped to the opposite side of the cell during the simulation.

1.1. Composition of the system

The components of the system are shown in the table below.

TypeNumber
Protein molecules1
Protein residues346
Protein atoms5648
Nucleic acid molecules0
Nucleic acid residues0
Nucleic acid atoms0
Residue Mrv with 79 atoms1
Residue Pea with 125 atoms184
Element Zn1
Element Cl47
Element Na45
Water residues15552
Total number of atoms75476

Table-1: Composition of the simulated system

Object 1 with name 4mbs has been identified as the solute and is shown below. If this is not the intended solute, please change the soluteobj variable in this macro.

Figure-2: The solute oriented along the major axes.

1.2. The ligand

A special ligand analysis has been performed for MRV, chosen automatically by YASARA with the selection Res MRV. The number of residues matching the ligand selection is 1, with 79 atoms. To change the ligand selection, edit the ligandsel variable at the beginning of this macro.

Figure-3: A ray-traced picture of the ligand MRV. Bonds are colored by their order: Gray = 1, blue = 1.25, magenta = 1.33, red = 1.5, orange = 1.66, bright orange = 1.75, yellow = 2, lime green = 2.5, green = 3 and cyan = 4.

2. Analysis inside the simulation cell

This section shows all analyses that have been performed inside the simulation cell, when all atoms share the common coordinate system of the simulation cell.

Periodic boundaries are active and considered for distance measurements. Calculations that involve groups of atoms [center of mass, regression lines, enclosing spheres..] are ambiguous and should be placed in the next section, unless it is known that the atom group does not drift through a periodic boundary.

2.1. Simulation cell lengths

Conformational changes of the simulated solute molecules lead to fluctuations in density. If the simulation box has a constant size, changes in density lead to changes in pressure. This is not realistic, because molecules normally "live" in a constant pressure environment. During the simulation the cell is therefore rescaled to maintain a constant cell pressure. Depending on the chosen pressure control mode, the three cell axes are either rescaled together [Manometer1D], partly together [X- and Z-axes, Manometer2D, used for membrane simulations], independently [Manometer3D], or not at all [Off]. You can deduce the pressure control mode from the plot below.

Figure-4: Simulation cell lengths [vertical axis] as a function of simulation time [horizontal axis]. Note: Graph CellLengthZ completely covers graph CellLengthX, they share the same values.

2.2. Total potential energy of the system

The total potential energy of the system is plotted, according to the AMBER14 force field. If you ran the simulation with a different force field, you need to adapt the ForceField command at the top of this macro accordingly.

When the simulation is started from an energy-minimized "frozen" conformation, there is usually a sharp increase in energy during the first picoseconds, since the added kinetic energy is partly stored as potential energy. Also on a larger time-scale, the potential energy will often not decrease. A common reason are counter ions. These are initially placed at the positions with the lowest potential energy, usually close to charged solute groups, from where they detach to gain entropy, but also potential energy.

Figure-5: Total potential energy of the system [vertical axis] as a function of simulation time [horizontal axis]. Note: The first value of the plot [-982296.25], coming from the energy minimized starting structure, has been replaced with the second value of the plot [-783131.63] to show this plot with a smaller energy range and thus a higher resolution.

2.3. Potential energy components

The following individual components of the total potential energy are plotted: bond energies [Bond], bond angle energies [Angle], dihedral angle energies [Dihedral], planarity or improper dihedral energies [Planarity], Van der Waals energies [VdW] and electrostatic energies [Coulomb]. Force field energies help to judge the structural quality of a protein: distortions of local covalent geometry can be found by looking at the bond, angle and planarity energies. Unrealistically close contacts [bumps] lead to a high Van der Waals energy, just like a large number of hydrogen bonds [since they pull the atoms closer than their normal Van der Waals contact distance]. The Coulomb energy is the least informative, because it strongly depends on the amino acid composition [e.g. proteins with a net charge have a higher Coulomb energy].

Figure-6: Potential energy components [vertical axis] as a function of simulation time [horizontal axis].

2.4. Protein secondary structure content

The total percentages of alpha helices, beta sheets, turns, coils, 3-10 helices and pi helices are calculated and plotted. For clarification, a turn is simply a stretch of four residues that are not part of other secondary structure elements and form a hydrogen bond between the O of the first and the NH of the last residue. A coil is anything that does not fit into the other categories. Note that pi-helices [helices with hydrogen bonds between residues N and N+5] are rather unstable and thus do not normally occur in proteins, except for short bulges in alpha helices [which are often the result of single residue insertions and prolines].

Figure-7: Protein secondary structure content [vertical axis] as a function of simulation time [horizontal axis], obtained with the command "SecStr". Note: Graph PiHelix has all zero values.

2.5. Surface areas of the solute

The Van der Waals [SurfVdW], molecular [SurfMol] and solvent accessible [SurfAcc] surface areas of the solute in A^2 are plotted. The difference between these surface types can be summarized as follows:

Van der Waals surface: if you think of atoms as spheres with a given Van der Waals radius, then the Van der Waals surface consists of all the points on these spheres that are not inside another sphere. In practice, the Van der Waals surface is of limited use, because it can be found throughout a protein and does not tell much about the interaction with the solvent.

Molecular surface: this is the Van der Waals surface from the viewpoint of a solvent molecule, which is a much more useful concept. The water is assumed to be a sphere of a given radius [also called the water probe], that rolls over the solute. Those parts of the Van der Waals surface that the water probe can touch are simply copied to the molecular surface [and called the contact surface]. Clefts in the Van der Waals surface that are too narrow for the water probe to enter are replaced by the Van der Waals surface of the water probe itself [and called the reentrant surface]. So the molecular surface is a smooth composition of two Van der Waals surfaces: the one of the solute and the one of the solvent molecule while it traces the contours of the solute. Other common names for the molecular surface are solvent excluded surface or Connolly surface.

Solvent accessible surface: this surface consists of all the points that the center of the water probe [i.e. the nucleus of the oxygen atom in the water molecule] can reach while rolling over the solute. The shortest possible distance between the water oxygen nucleus and a solute atom is simply the sum of the Van der Waals radii of the solute atom and the water probe.

Figure-8: Surface areas of the solute [vertical axis] as a function of simulation time [horizontal axis], obtained with the command "SurfObj Solute".

2.6. Number of hydrogen bonds in the solute

The number of hydrogen bonds inside the solute is plotted below. One hydrogen bond per hydrogen atom is assigned at most, picking the better one if two acceptors are available.The following formula yields the bond energy in [kJ/mol] as a function of the Hydrogen-Acceptor distance in [A] and two scaling factors:

The first scaling factor depends on the angle formed by Donor-Hydrogen-Acceptor:

The second scaling factor is derived from the angle formed by Hydrogen-Acceptor-X, where X is the atom covalently bound to the acceptor. If X is a heavy atom:

If X is a hydrogen, slightly smaller angles are allowed:

A hydrogen bond is counted if the hydrogen bond energy obtained with this formula is better than 6.25 kJ/mol [or 1.5 kcal/mol], which is 25% of the optimum value 25 kJ/mol.

Figure-9: Number of hydrogen bonds in the solute [vertical axis] as a function of simulation time [horizontal axis].

2.7. Number of hydrogen bonds between solute and solvent

The plot shows the number of hydrogen bonds between solute and solvent. Together with the plot above, it is a good indicator for successful protein folding, indicated by a decreasing number of bonds with the solvent and a growing number of bonds within the solute.

Figure-10: Number of hydrogen bonds between solute and solvent [vertical axis] as a function of simulation time [horizontal axis].

2.8. Hydrogen bonds made by Res MRV

The following table shows all hydrogen bonds made by Res MRV. With 6 acceptors and 2 donors, a total number of 14 hydrogen bonds are possible - labeled HB1 to HB14.The first atom of the bonding pair is labeled Atm1 and the second Atm2, respectively. The atom ID separates atom name, residue ID and molecule name with dots. A lower-case "h" indicates hetgroups. E and D are short for the hydrogen bonding energy in [ kJ/mol ] and the distance between the bonding partners in [A]. To list other hydrogen bonds, edit the hbosel variable at the beginning of this macro.

Time [ns]HB1Atm1HB1Atm2HB1EHB1DHB2Atm1HB2Atm2HB2EHB2DHB3Atm1HB3Atm2HB3EHB3DHB4Atm1HB4Atm2HB4EHB4DHB5Atm1HB5Atm2HB5EHB5DHB6Atm1HB6Atm2HB6EHB6DHB7Atm1HB7Atm2HB7EHB7DHB8Atm1HB8Atm2HB8EHB8DHB9Atm1HB9Atm2HB9EHB9DHB10Atm1HB10Atm2HB10EHB10DHB11Atm1HB11Atm2HB11EHB11DHB12Atm1HB12Atm2HB12EHB12DHB13Atm1HB13Atm2HB13EHB13DHB14Atm1HB14Atm2HB14EHB14D
0.00N2.h1101.AOE1.E283.A23.451.70N3.h1101.AOH.Y37.A25.001.91N5.h1101.AOH.Y251.A18.302.11--------------------------------------------
2.50N2.h1101.AOE1.E283.A25.001.76N3.h1101.AOH.Y37.A25.001.85------------------------------------------------
5.00N2.h1101.AOE1.E283.A22.271.87N3.h1101.AOH.Y37.A17.601.81------------------------------------------------
7.50N2.h1101.AOE1.E283.A21.881.72N3.h1101.AOH.Y37.A21.502.00N5.h1101.AOH.Y251.A25.002.00--------------------------------------------
10.00N2.h1101.AOE1.E283.A19.931.82N3.h1101.AOH.Y37.A21.881.84------------------------------------------------
12.50N2.h1101.AOE1.E283.A17.601.85N3.h1101.AOH.Y37.A23.851.95------------------------------------------------
15.00N2.h1101.AOE1.E283.A22.271.68N3.h1101.AOH.Y37.A7.722.17------------------------------------------------
17.50N2.h1101.AOE1.E283.A24.431.76N3.h1101.AOH.Y37.A25.001.74------------------------------------------------
20.00N2.h1101.AOE1.E283.A20.731.79N3.h1101.AOH.Y37.A25.001.81------------------------------------------------
22.50N2.h1101.AOE1.E283.A20.731.72N3.h1101.AOH.Y37.A25.001.87------------------------------------------------

Table-2: Hydrogen bonds made by Res MRV as a function of simulation time [first column]. Note: At most 10 table rows are shown. Change the tabrowsmax variable in the macro to adjust the number of shown table rows. The full table can be found in 4mbs_analysis.tab.

3. Analysis outside the simulation cell

The following section presents data gathered outside the simulation cell, where each object has its own local coordinate systems and no periodic boundaries are present. Calculations that involve the interaction between objects [common surface areas, contacts between objects..] must be placed in the previous section.

3.1. Radius of gyration of the solute

After determining the center of mass of the solute, the radius of gyration is calculated and plotted according to this formula:

In this formula, C is the center of mass, and Ri is the position of atom i of N.

Figure-11: Radius of gyration of the solute [vertical axis] as a function of simulation time [horizontal axis], obtained with the command "RadiusObj Solute,Center=Mass,Type=Gyration".

4. Analyses performed with respect to the starting structure

Analyses performed with respect to the starting structure are shown in this section. These are also done outside the simulation cell, where each object has its own local coordinate systems and no periodic boundaries are present. To choose another reference snapshot than 0, edit the refsnapshot variable at the beginning of this macro.

4.1. Solute RMSD from the starting structure

The plot shows Calpha [RMSDCa], backbone [RMSDBb] and all-heavy atom [RMSDAll] RMSDs calculated according to this formula, where Ri is the vector linking the positions of atom i [of N atoms] in the reference snapshot and the current snapshot after optimal superposition:

The selection for the Calpha RMSD calculation is CA Protein or C1* NucAcid, this matched 346 atoms. The Calpha selection thus includes the main backbone carbon C1* of nucleic acids, so the plot also shows a Calpha RMSD if you simulate just nucleic acids. In simulations of protein-DNA complexes, the Calpha RMSD therefore considers the DNA too. To change the Calpha selection, edit the casel variable at the beginning of this macro.

Figure-12: Solute RMSD from the starting structure [vertical axis] as a function of simulation time [horizontal axis].

4.2. Ligand movement RMSD after superposing on the receptor

The following plot shows the RMSD of the ligand heavy atoms over time, measured after superposing the receptor on its reference structure. This procedure delivers information about the movement of the ligand in its binding pocket.

Figure-13: Ligand movement RMSD after superposing on the receptor [vertical axis] as a function of simulation time [horizontal axis].

4.3. Ligand conformation RMSD after superposing on the ligand

This plot displays the RMSD of the ligand atoms over time, measured after superposing on the reference structure of the ligand. The gained data summarize the conformational changes of the ligand.

Figure-14: Ligand conformation RMSD after superposing on the ligand [vertical axis] as a function of simulation time [horizontal axis].

5. Dynamic Cross-Correlation Matrix

The dynamic cross-correlation matrix [DCCM] is a square matrix, whose rows and columns match the selected units Atom CA Protein. To change this selection, edit the dccmsel variable at the beginning of this macro. The DCCM shows how the movements of all selected pairs correlate. The values in the DCCM range from -1 [perfectly anti-correlated] to +1 [perfectly correlated]. The values along the diagonal are always +1 [because the motion of an atom is perfectly correlated to itself]. The DCCM element for units i and j is obtained with the following formula:

Here d is the displacement between the current position and the average position of the selected unit, and the angle brackets indicate the average over all samples. The highest correlations off the diagonal can often be found for bridged cysteines.

The image below shows the correlation directly in the solute object:

Figure-15: Blue and red lines are shown between strongly anti- and correlated pairs. To change the threshold value for the correlation lines edit the dccmcut variable at the beginning of this macro. To look at this structure interactively, open the file 4mbs_dccm.yob in YASARA.

In the image below, the DCCM is visualized with colors ranging from blue [-1, fully anti-correlated] to yellow [+1, fully correlated]. The zero level [0, not correlated] is indicated with a wire-frame grid.

Figure-16: Visualization of the dynamic cross-correlation matrix. Open the file 4mbs_dccm.sce in YASARA to look at this matrix visualization interactively.

DCCMA
Pro
19
A
Cys
20
A
Gln
21
A
Lys
22
A
Ile
23
A
Asn
24
A
Val
25
A
Lys
26
A
Gln
27
A
Ile
28
A
Ala
29
A
Ala
30
A
Arg
31
A
Leu
32
A
Leu
33
A
Pro
34
A
Pro
35
A
Leu
36
A
Tyr
37
A
Ser
38
A
Leu
39
A
Val
40
A
Phe
41
A
Ile
42
A
Phe
43
A
Gly
44
A
Phe
45
A
Val
46
A
Gly
47
A
Asn
48
A
Met
49
A
Leu
50
A
Val
51
A
Ile
52
A
Leu
53
A
Ile
54
A
Leu
55
A
Ile
56
A
Asn
57
A
Tyr
58
A
Lys
59
A
Arg
60
A
Leu
61
A
Lys
62
A
Ser
63
A
Met
64
A
Thr
65
A
Asp
66
A
Ile
67
A
Tyr
68
A
Leu
69
A
Leu
70
A
Asn
71
A
Leu
72
A
Ala
73
A
Ile
74
A
Ser
75
A
Asp
76
A
Leu
77
A
Phe
78
A
Phe
79
A
Leu
80
A
Leu
81
A
Thr
82
A
Val
83
A
Pro
84
A
Phe
85
A
Trp
86
A
Ala
87
A
His
88
A
Tyr
89
A
Ala
90
A
Ala
91
A
Ala
92
A
Gln
93
A
Trp
94
A
Asp
95
A
Phe
96
A
Gly
97
A
Asn
98
A
Thr
99
A
Met
100
A
Cys
101
A
Gln
102
A
Leu
103
A
Leu
104
A
Thr
105
A
Gly
106
A
Leu
107
A
Tyr
108
A
Phe
109
A
Ile
110
A
Gly
111
A
Phe
112
A
Phe
113
A
Ser
114
A
Gly
115
A
Ile
116
A
Phe
117
A
Phe
118
A
Ile
119
A
Ile
120
A
Leu
121
A
Leu
122
A
Thr
123
A
Ile
124
A
Asp
125
A
Arg
126
A
Tyr
127
A
Leu
128
A
Ala
129
A
Val
130
A
Val
131
A
His
132
A
Ala
133
A
Val
134
A
Phe
135
A
Ala
136
A
Leu
137
A
Lys
138
A
Ala
139
A
Arg
140
A
Thr
141
A
Val
142
A
Thr
143
A
Phe
144
A
Gly
145
A
Val
146
A
Val
147
A
Thr
148
A
Ser
149
A
Val
150
A
Ile
151
A
Thr
152
A
Trp
153
A
Val
154
A
Val
155
A
Ala
156
A
Val
157
A
Phe
158
A
Ala
159
A
Ser
160
A
Leu
161
A
Pro
162
A
Asn
163
A
Ile
164
A
Ile
165
A
Phe
166
A
Thr
167
A
Arg
168
A
Ser
169
A
Gln
170
A
Lys
171
A
Glu
172
A
Gly
173
A
Leu
174
A
His
175
A
Tyr
176
A
Thr
177
A
Cys
178
A
Ser
179
A
Ser
180
A
His
181
A
Phe
182
A
Pro
183
A
Tyr
184
A
Ser
185
A
Gln
186
A
Tyr
187
A
Gln
188
A
Phe
189
A
Trp
190
A
Lys
191
A
Asn
192
A
Phe
193
A
Gln
194
A
Thr
195
A
Leu
196
A
Lys
197
A
Ile
198
A
Val
199
A
Ile
200
A
Leu
201
A
Gly
202
A
Leu
203
A
Val
204
A
Leu
205
A
Pro
206
A
Leu
207
A
Leu
208
A
Val
209
A
Met
210
A
Val
211
A
Ile
212
A
Cys
213
A
Tyr
214
A
Ser
215
A
Gly
216
A
Ile
217
A
Leu
218
A
Lys
219
A
Thr
220
A
Leu
221
A
Leu
222
A
Arg
223
A
Met
1001
A
Lys
1002
A
Lys
1003
A
Tyr
1004
A
Thr
1005
A
Cys
1006
A
Thr
1007
A
Val
1008
A
Cys
1009
A
Gly
1010
A
Tyr
1011
A
Ile
1012
A
Tyr
1013
A
Asn
1014
A
Pro
1015
A
Glu
1016
A
Asp
1017
A
Gly
1018
A
Asp
1019
A
Pro
1020
A
Asp
1021
A
Asn
1022
A
Gly
1023
A
Val
1024
A
Asn
1025
A
Pro
1026
A
Gly
1027
A
Thr
1028
A
Asp
1029
A
Phe
1030
A
Lys
1031
A
Asp
1032
A
Ile
1033
A
Pro
1034
A
Asp
1035
A
Asp
1036
A
Trp
1037
A
Val
1038
A
Cys
1039
A
Pro
1040
A
Leu
1041
A
Cys
1042
A
Gly
1043
A
Val
1044
A
Gly
1045
A
Lys
1046
A
Asp
1047
A
Gln
1048
A
Phe
1049
A
Glu
1050
A
Glu
1051
A
Val
1052
A
Glu
1053
A
Glu
1054
A
Glu
227
A
Lys
228
A
Lys
229
A
Arg
230
A
His
231
A
Arg
232
A
Asp
233
A
Val
234
A
Arg
235
A
Leu
236
A
Ile
237
A
Phe
238
A
Thr
239
A
Ile
240
A
Met
241
A
Ile
242
A
Val
243
A
Tyr
244
A
Phe
245
A
Leu
246
A
Phe
247
A
Trp
248
A
Ala
249
A
Pro
250
A
Tyr
251
A
Asn
252
A
Ile
253
A
Val
254
A
Leu
255
A
Leu
256
A
Leu
257
A
Asn
258
A
Thr
259
A
Phe
260
A
Gln
261
A
Glu
262
A
Phe
263
A
Phe
264
A
Gly
265
A
Leu
266
A
Asn
267
A
Asn
268
A
Cys
269
A
Ser
270
A
Ser
271
A
Ser
272
A
Asn
273
A
Arg
274
A
Leu
275
A
Asp
276
A
Gln
277
A
Ala
278
A
Met
279
A
Gln
280
A
Val
281
A
Thr
282
A
Glu
283
A
Thr
284
A
Leu
285
A
Gly
286
A
Met
287
A
Thr
288
A
His
289
A
Cys
290
A
Cys
291
A
Ile
292
A
Asn
293
A
Pro
294
A
Ile
295
A
Ile
296
A
Tyr
297
A
Ala
298
A
Phe
299
A
Val
300
A
Gly
301
A
Glu
302
A
Glu
303
A
Phe
304
A
Arg
305
A
Asn
306
A
Tyr
307
A
Leu
308
A
Leu
309
A
Val
310
A
Phe
311
A
Phe
312
A
Gln
313
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A-Asn-240.090.330.470.650.841.000.700.590.540.560.030.190.190.140.170.280.270.220.220.250.180.100.120.130.02-0.05-0.13-0.19-0.18-0.23-0.27-0.27-0.29-0.31-0.27-0.29-0.32-0.25-0.22-0.26-0.33-0.32-0.32-0.32-0.36-0.35-0.40-0.43-0.40-0.36-0.38-0.36-0.33-0.34-0.23-0.17-0.23-0.140.04-0.03-0.080.030.030.110.170.210.200.180.220.220.110.110.170.130.04-0.010.07-0.050.040.070.080.060.070.060.01-0.020.07-0.00-0.03-0.02-0.17-0.20-0.16-0.21-0.36-0.33-0.28-0.28-0.38-0.37-0.32-0.37-0.38-0.35-0.36-0.34-0.35-0.35-0.30-0.31-0.31-0.29-0.31-0.34-0.35-0.37-0.45-0.43-0.33-0.34-0.37-0.37-0.36-0.31-0.30-0.36-0.36-0.29-0.30-0.34-0.33-0.27-0.27-0.30-0.27-0.24-0.29-0.31-0.22-0.25-0.30-0.26-0.15-0.22-0.13-0.02-0.010.020.100.140.110.130.080.070.02-0.010.040.110.150.150.120.100.100.020.020.110.130.020.06-0.03-0.14-0.13-0.09-0.20-0.26-0.27-0.28-0.34-0.37-0.36-0.32-0.42-0.42-0.32-0.30-0.39-0.43-0.34-0.34-0.41-0.40-0.32-0.35-0.40-0.34-0.25-0.31-0.34-0.25-0.22-0.19-0.22-0.32-0.25-0.20-0.31-0.31-0.30-0.21-0.21-0.10-0.16-0.09-0.09-0.08-0.00-0.070.05-0.020.120.050.140.260.290.310.310.330.360.360.330.250.220.320.150.150.100.270.290.250.190.220.250.210.180.230.160.120.170.100.120.100.01-0.05-0.09-0.21-0.26-0.34-0.28-0.35-0.34-0.36-0.31-0.35-0.29-0.18-0.12-0.23-0.22-0.25-0.27-0.22-0.20-0.22-0.22-0.17-0.15-0.15-0.15-0.11-0.11-0.16-0.21-0.10-0.11-0.22-0.15-0.04-0.09-0.100.020.10-0.01-0.050.050.170.210.090.100.140.030.410.520.490.370.420.500.390.300.400.410.240.180.280.230.070.070.150.06-0.030.040.09-0.02-0.010.05-0.03-0.12-0.08-0.06-0.16-0.13-0.02-0.11-0.20-0.29-0.19-0.16-0.28-0.130.080.080.050.210.260.270.270.23
A-Val-250.250.430.330.420.610.701.000.780.780.710.060.340.430.340.290.450.490.370.390.490.380.240.330.350.150.080.090.00-0.04-0.12-0.07-0.12-0.22-0.23-0.13-0.21-0.30-0.21-0.12-0.20-0.31-0.29-0.37-0.39-0.48-0.53-0.57-0.53-0.51-0.53-0.47-0.40-0.40-0.44-0.21-0.13-0.26-0.070.180.070.030.240.240.330.390.450.430.360.430.450.300.280.360.290.200.200.300.270.290.260.250.320.320.220.220.290.280.120.150.15-0.14-0.20-0.09-0.25-0.47-0.50-0.43-0.45-0.63-0.61-0.56-0.61-0.63-0.61-0.59-0.58-0.61-0.60-0.52-0.53-0.55-0.53-0.54-0.56-0.58-0.54-0.50-0.58-0.54-0.52-0.55-0.59-0.55-0.47-0.47-0.54-0.54-0.46-0.47-0.54-0.49-0.41-0.45-0.49-0.41-0.41-0.50-0.46-0.34-0.44-0.50-0.36-0.26-0.35-0.190.08-0.000.040.200.280.280.210.140.110.050.050.130.230.320.350.260.180.170.070.070.160.140.050.130.06-0.12-0.11-0.01-0.18-0.31-0.24-0.20-0.36-0.46-0.46-0.41-0.55-0.55-0.46-0.46-0.55-0.59-0.54-0.54-0.58-0.59-0.54-0.55-0.60-0.57-0.47-0.50-0.54-0.48-0.43-0.45-0.48-0.51-0.48-0.42-0.46-0.52-0.50-0.37-0.32-0.14-0.24-0.12-0.11-0.24-0.03-0.140.090.010.230.130.270.430.480.490.500.530.550.550.510.410.340.470.180.200.140.390.460.430.330.400.430.370.320.400.300.240.310.200.230.180.04-0.04-0.12-0.33-0.45-0.54-0.49-0.57-0.59-0.61-0.57-0.61-0.53-0.39-0.38-0.45-0.45-0.43-0.48-0.46-0.42-0.40-0.40-0.35-0.31-0.32-0.28-0.22-0.21-0.29-0.34-0.18-0.17-0.35-0.29-0.10-0.24-0.36-0.18-0.03-0.28-0.300.160.220.030.100.330.160.160.520.640.570.480.560.630.490.430.560.500.310.290.410.290.080.100.210.05-0.090.000.02-0.13-0.120.02-0.09-0.21-0.09-0.07-0.25-0.19-0.02-0.14-0.33-0.44-0.30-0.25-0.37-0.220.030.090.060.240.410.450.430.40
A-Lys-260.100.250.170.110.430.590.781.000.890.67-0.100.220.280.170.120.290.340.200.240.400.270.140.300.340.110.060.150.080.03-0.120.050.02-0.09-0.080.04-0.04-0.11-0.010.06-0.02-0.12-0.06-0.13-0.16-0.26-0.31-0.38-0.31-0.23-0.28-0.29-0.18-0.14-0.25-0.080.06-0.06-0.010.270.190.090.270.300.350.370.420.430.330.360.390.300.230.310.270.240.210.290.270.330.280.330.340.320.280.310.340.300.210.240.18-0.07-0.030.00-0.22-0.39-0.33-0.40-0.40-0.51-0.50-0.53-0.55-0.53-0.56-0.54-0.52-0.56-0.50-0.47-0.48-0.50-0.50-0.53-0.50-0.46-0.40-0.38-0.41-0.33-0.33-0.32-0.39-0.30-0.24-0.22-0.27-0.27-0.17-0.18-0.26-0.20-0.11-0.18-0.22-0.12-0.13-0.25-0.23-0.08-0.20-0.32-0.17-0.04-0.16-0.120.160.140.100.230.270.270.230.190.210.170.150.180.220.300.340.220.140.140.080.110.160.110.070.100.05-0.06-0.10-0.08-0.19-0.26-0.28-0.28-0.37-0.44-0.44-0.45-0.51-0.49-0.44-0.50-0.57-0.55-0.55-0.57-0.60-0.59-0.58-0.61-0.61-0.60-0.57-0.59-0.59-0.55-0.54-0.54-0.53-0.52-0.50-0.40-0.33-0.39-0.48-0.19-0.160.07-0.000.100.01-0.21-0.08-0.25-0.02-0.26-0.02-0.21-0.060.200.300.310.350.460.440.430.320.130.080.370.340.390.400.520.560.570.530.560.550.510.420.380.290.340.450.420.460.430.350.260.17-0.05-0.22-0.43-0.40-0.53-0.66-0.69-0.65-0.61-0.65-0.63-0.52-0.49-0.49-0.44-0.53-0.53-0.51-0.48-0.49-0.47-0.45-0.46-0.42-0.37-0.39-0.45-0.51-0.42-0.40-0.51-0.49-0.37-0.41-0.48-0.39-0.22-0.31-0.40-0.120.170.04-0.080.08-0.000.080.220.320.170.060.210.260.060.030.250.14-0.080.030.17-0.03-0.21-0.100.00-0.17-0.23-0.07-0.07-0.24-0.17-0.08-0.19-0.25-0.06-0.13-0.31-0.19-0.05-0.22-0.37-0.37-0.38-0.38-0.46-0.220.060.140.110.290.430.440.360.34
A-Gln-270.110.250.130.080.380.540.780.891.000.81-0.020.330.420.310.260.420.470.320.350.500.370.220.370.400.140.080.160.05-0.01-0.14-0.00-0.06-0.18-0.17-0.06-0.15-0.24-0.13-0.05-0.13-0.25-0.19-0.27-0.30-0.40-0.45-0.50-0.44-0.37-0.42-0.41-0.31-0.27-0.37-0.16-0.03-0.16-0.050.260.150.090.300.330.400.430.500.500.410.460.490.370.320.410.330.290.260.330.280.360.310.340.380.390.310.330.380.350.220.240.21-0.07-0.08-0.03-0.24-0.47-0.43-0.47-0.51-0.61-0.60-0.62-0.63-0.62-0.64-0.62-0.58-0.61-0.58-0.52-0.52-0.55-0.55-0.59-0.57-0.53-0.49-0.46-0.46-0.40-0.40-0.40-0.50-0.43-0.36-0.33-0.40-0.42-0.30-0.31-0.39-0.35-0.24-0.30-0.36-0.26-0.25-0.37-0.35-0.19-0.30-0.41-0.25-0.11-0.24-0.120.160.110.100.260.320.320.280.220.230.170.130.200.260.390.420.310.190.180.080.120.180.120.060.100.04-0.08-0.11-0.07-0.20-0.28-0.29-0.28-0.38-0.46-0.48-0.48-0.57-0.54-0.49-0.54-0.62-0.62-0.61-0.63-0.66-0.66-0.63-0.66-0.68-0.65-0.57-0.61-0.64-0.57-0.54-0.57-0.57-0.55-0.55-0.48-0.43-0.48-0.54-0.27-0.24-0.00-0.090.03-0.03-0.27-0.06-0.230.05-0.160.12-0.090.080.350.440.450.480.570.570.570.470.280.230.520.400.440.410.590.640.620.550.600.610.550.470.470.350.360.480.410.450.420.290.190.09-0.16-0.35-0.55-0.53-0.65-0.75-0.74-0.71-0.67-0.70-0.66-0.58-0.55-0.56-0.51-0.59-0.58-0.55-0.51-0.53-0.50-0.47-0.47-0.43-0.38-0.39-0.46-0.52-0.41-0.39-0.52-0.49-0.36-0.40-0.47-0.38-0.20-0.28-0.37-0.110.180.02-0.080.05-0.080.120.290.390.260.150.270.340.150.100.320.23-0.000.070.250.04-0.16-0.050.09-0.12-0.20-0.03-0.06-0.24-0.19-0.05-0.17-0.28-0.09-0.13-0.33-0.26-0.09-0.23-0.43-0.46-0.41-0.42-0.44-0.180.070.180.210.390.520.530.470.43

Table-3: Dynamic cross-correlation matrix. The full table is also available in text format, you need a proper text editor without line wrapping to look at this file: 4mbs_dccm.tab. Note: At most 10 rows of the DCCM are shown above. Change the tabrowsmax variable in the macro to adjust this number.

6. Additional files

The following additional files have been created:

6.1. The main data table

The main table contains all collected data in a single file. The column names match the names used above for graphs in plots and columns in tables. You can find a more detailed explanation of this table in the user manual at Recipes > Run a molecular dynamics simulation > Analyzing a trajectory. If you parse this file automatically, keep in mind that the number of columns can change any time, so you have to use the names in the first table row to find the columns of interest: 4mbs_analysis.tab

6.2. The structures

The time averaged structure in PDB format: 4mbs_average.pdb

The snapshot with the minimum solute energy. Either just the solute in PDB format 4mbs_energymin.pdb, or the complete system including solvent as a YASARA scene 4mbs_energymin.sce.

The last snapshot of the simulation. Either just the solute in PDB format 4mbs_last.pdb, or the complete system including solvent as a YASARA scene 4mbs_last.sce

6.3. The RMSF table

A table that lists the Root Mean Square Fluctuations [RMSFs] of all atoms in [A] is available here: 4mbs_rmsf.tab. The RMSFs have also been converted to B-factors and stored in the B-factor field of the time-average structure above.

6.4. High resolution plots

To facilitate publication, high resolution versions of the plots above have been created with a 4:3 aspect ratio suited for printing in a single column of a typical journal article. Just look at the figure number above to find the right file:

4mbs_report_figure4_hires.png

4mbs_report_figure5_hires.png

4mbs_report_figure6_hires.png

4mbs_report_figure7_hires.png

4mbs_report_figure8_hires.png

4mbs_report_figure9_hires.png

4mbs_report_figure10_hires.png

4mbs_report_figure11_hires.png

4mbs_report_figure12_hires.png

4mbs_report_figure13_hires.png

4mbs_report_figure14_hires.png