SpINPHARMA

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Software availability

Spinpharma is now available (and free for Academia) upon request by sending an email to: software@nmr.mpibpc.mpg.de

Introduction

SpINPHARMA is a program for evaluation of INPHARMA experiments. The core functionality of the program is back-calculation of NOESY spectra for mixtures of two ligands and protein of interest.

The program uses complete relaxation matrix approach:

\[\dfrac{d \mathbf{I}(\tau_m)}{dt} = - \mathbf{D} \mathbf{I}(\tau_m)\]

where

\[\mathbf{D} = \mathbf{R} + \mathbf{K}\]

\[\mathbf{I}(\tau_m) = e^{-\mathbf{D}\tau_m} \, \mathbf{I}(0)\]

\[\mathbf{D}\] is a dynamic matrix

\[\mathbf{R}\] is a relaxation matrix

\[\mathbf{K}\] is a kinetic matrix

The peak integrals are calculated using eigendecomposition.

Kinetic models

Model 1

\[TL_1 + L_2 \rightleftarrows L_1 + T + L_2 \rightleftarrows TL_2 + L_1\]

Kinetic rate constants

\[k_{1off}\], \(k_{1on}\), \(k_{2off}\) and \(k_{2on}\)

For the 'Model 1' the kinetic matrix \(K\) is

\[\mathbf{K} = \left( \begin{array}{rrrrrrr} k_{1on}[T]\mathbf{I} & 0 & -k_{1off}\mathbf{I} & 0 & 0 & 0 & 0 \\ 0 & k_{2on}[T]\mathbf{I} & 0 & 0 & -k_{2off}\mathbf{I} & 0 & 0 \\ -k_{1on}[T]\mathbf{I} & 0 & k_{1off}\mathbf{I} & 0 & 0 & 0 & 0 \\ 0 & 0 & 0 & k_{1off}\mathbf{I} & 0 & 0 & -k_{1on}[L_1]\mathbf{I} \\ 0 & -k_{2on}[T]\mathbf{I} & 0 & 0 & k_{2off}\mathbf{I} & 0 & 0 \\ 0 & 0 & 0 & 0 & 0 & k_{2off}\mathbf{I} & -k_{2on}[L_2]\mathbf{I} \\ 0 & 0 & 0 & -k_{1off}\mathbf{I} & 0 & -k_{2off}\mathbf{I} & k_{1on}[L_1]\mathbf{I} + k_{2on}[L_2]\mathbf{I} \end{array} \right)\]


Model 2

\[TL_1 + L_2 \rightleftarrows TL_2 + L_1\]

Kinetic rate constants

\[k_{L1}\] and \(k_{L2}\)

For the 'Model 2' the kinetic matrix \(K\) is \[\mathbf{K} = \left( \begin{array}{rrrrrrr} k_{L2}[TL_2]\mathbf{I} & 0 & -k_{L1}[L_2]\mathbf{I} & 0 & 0 & 0 \\ 0 & k_{L1}[TL_1]\mathbf{I} & 0 & 0 & -k_{L2}[L_1]\mathbf{I} & 0 \\ -k_{L2}[TL_2]\mathbf{I} & 0 & k_{L1}[L_2]\mathbf{I} & 0 & 0 & 0 \\ 0 & 0 & 0 & k_{L1}[L_2]\mathbf{I} & 0 & -k_{L2}[L_1]\mathbf{I} \\ 0 & -k_{L1}[TL_1]\mathbf{I} & 0 & 0 & k_{L2}[L_1]\mathbf{I} & 0 \\ 0 & 0 & 0 & -k_{L1}[L_2]\mathbf{I} & 0 & k_{L2}[L_1]\mathbf{I}\\ \end{array} \right)\]

Relaxation models

for kinetic model 1 \[\mathbf{R} = \left( \begin{array}{rrrrrrr} \mathbf{R}^{L_1}_{L_1} & 0 & 0 & 0 & 0 & 0 & 0 \\ 0 & \mathbf{R}^{L_2}_{L_2} & 0 & 0 & 0 & 0 & 0 \\ 0 & 0 & \mathbf{R}^{TL_1}_{L_1} & \mathbf{R}^{TL_1}_{L_1,T} & 0 & 0 & 0 \\ 0 & 0 & \mathbf{R}^{TL_1}_{T,L_1} & \mathbf{R}^{TL_1}_{T} & 0 & 0 & 0 \\ 0 & 0 & 0 & 0 & \mathbf{R}^{TL_2}_{L_2} & \mathbf{R}^{TL_2}_{L2,T} & 0 \\ 0 & 0 & 0 & 0 & \mathbf{R}^{TL_2}_{T,L_2} & \mathbf{R}^{TL_2}_{T} & 0 \\ 0 & 0 & 0 & 0 & 0 & 0 & \mathbf{R}^{T}_{T} \end{array} \right)\]

for kinetic model 2 \[\mathbf{R} = \left( \begin{array}{rrrrrr} \mathbf{R}^{L_1}_{L_1} & 0 & 0 & 0 & 0 & 0 \\ 0 & \mathbf{R}^{L_2}_{L_2} & 0 & 0 & 0 & 0 \\ 0 & 0 & \mathbf{R}^{TL_1}_{L_1} & \mathbf{R}^{TL_1}_{L_1,T} & 0 & 0 \\ 0 & 0 & \mathbf{R}^{TL_1}_{T,L_1} & \mathbf{R}^{TL_1}_{T} & 0 & 0 \\ 0 & 0 & 0 & 0 & \mathbf{R}^{TL_2}_{L_2} & \mathbf{R}^{TL_2}_{L2,T}\\ 0 & 0 & 0 & 0 & \mathbf{R}^{TL_2}_{T,L_2} & \mathbf{R}^{TL_2}_{T}\\ \end{array} \right)\]

The elements of relaxation matrix $\mathbf{R}</math>

Auto-relaxation rate: \[R_{ii} = \rho_i = \sum\limits_j^{j \neq i} \frac{1}{16}\mu_0^2 \hbar^2 \gamma_H^4 \dfrac{1}{r_{ij}^6} \left( 6J(2\omega) + 3J(\omega) + J(0) \right)\]

Cross-relaxation rate: \[R_{ij} = \sigma_i = \frac{1}{16}\mu_0^2 \hbar^2 \gamma_H^4 \dfrac{1}{r_{ij}^6} \left( 6J(2\omega) - J(0) \right)\]

Spectral density: \[J(\omega) = \dfrac{2}{5} \dfrac{S_{ij}^2 \tau_c}{1+\omega^2 \tau_c^2}\]

Methyl groups (N-site jump model): \[r_{ij,eff} = \left( \dfrac{1}{2N^2} \sum\limits_{a=1}^N \sum\limits_{b=1}^N \dfrac{3\vec{r}_{ij,a} \cdot\vec{r}_{ij,b} - r_{ij,a}^2 r_{ij,b}^2 } {r_{ij,a}^5 r_{ij,b}^5} \right)^{-\frac{1}{6}}\]

Running SpINPHARMA

SpINPHARMA uses OpenMP to support SMP parallelism. In order to control number of threads user should set the OMP_NUM_THREADS environment variable. For example, to run SpINPHARMA using 8 processors:

BASH shell
export OMP_NUM_THREADS=8
CSH shell
setenv OMP_NUM_THREADS 8

After setting the desired number of processors, SpINPHARMA can be started using command: 

spinpharma inph.conf

Configuration file

Configuration file provides the description of the INPHARMA experiment.

Input files and directories

Input_Directory, Output_Directory, Struct_Complex1_Directory, Struct_Complex2_Directory: describe the direcotries for input, output and PDB coordinate files, respectively.

Complex1_Pdb and Complex2_Pdb: PDB files for initial topology and assignment of hydrogens. The structures must have correct local geometry

HList_Ligand1,HList_Ligand2 and HList_Receptor: hydrogen lists for ligand 1, ligand 2 and protein

Struct_List_Complex1 and Struct_List_Complex2: plain text lists of PDB file names

Assignment_Ligand1 and Assignment_Ligand2: assignment files provide the link between NMR resonances and PDB atoms.

Experimental_Peaklist: experimental list of the observed peaks

The fileformats are described below.

Relaxation parameters

Spectrometer_Frequency: base frequency in Hz

Correlation_Time_of_L1Free, Correlation_Time_of_L2Free and Correlation_Time_of_Complexes correlation times in s/rad

Cutoff cut-off distance for protein hydrogens. The protein protons within given distance to one of the ligands are considered in the calculations

Kinetic parameters

Kinetic_Model: 1 or 2. Kinetic model 1 provides description of free while model 2 neglects it

KdL1 and KdL2 dissociation constants for complexes with ligand 1 and 2 (model 1 only)

kL1on and kL2on on-rates for the ligands (model 1 only)

kL1 and kL2 the corresponding rate constants (model 2 only)

Output options

Correlation_Output_Mode: selection for the correlation output: all, diag, intra or inter

Regression: choice of regression type: intercept or nointercept

Volumes_Output_Mode: choice for the volumes output: abs or norm

Correlation_Output, Volumes_Output and R_and_Qfactor_Output: output file names

Example

# Input Files
Input_Directory              .
Output_Directory           out

# Structures
Struct_Complex1_Directory   c1
Struct_Complex2_Directory   c2
Complex1_Pdb        pka_la.pdb
Complex2_Pdb        pka_lb.pdb

# Hydrogen lists
HList_Ligand1         la.hlist
HList_Ligand2         lb.hlist
HList_Receptor       pka.hlist

# Structures
Struct_List_Complex1    la.nam
Struct_List_Complex2    lb.nam

# Assignments
Assignment_Ligand1     la.asgn
Assignment_Ligand2     lb.asgn

# Relaxation Model Parameters
Spectrometer_Frequency         800.0e6   # [Hz]
Correlation_Time_of_L1Free       0.1e-9  # [s/rad]
Correlation_Time_of_L2Free       0.1e-9  # [s/rad]
Correlation_Time_of_Complexes   17.0e-9  # [s/rad]
Cutoff                           5.0     # [Angstrom]

# Kinetic Model and Parameters
Kinetic_Model        2
kL1            30000.0  # [l/(uM*s)] 1=10^6 [l/(M*s)]
kL2            10000.0  # [l/(uM*s)] 1=10^6 [l/(M*s)]

#Kinetic_Model       1
#KdL1           1000.0  # [uM]
#KdL2           3000.0  # [uM]
#kL1on           100.0  # [l/(uM*s)] 1=10^6 [l/(M*s)]
#kL2on           100.0  # [l/(uM*s)] 1=10^6 [l/(M*s)]

#Concentrations
cL1_tot          150.0  # [uM]
cL2_tot          450.0  # [uM]
cT_tot            25.0  # [uM]

#Experimental data
Experimental_Peaklist exp_norm.vols

#Output options and output files
Regression               intercept
Volumes_Output_Mode           norm
Correlation_Output_Mode      inter
Correlation_Output        corr.dat
R_and_Qfactor_Output      qual.dat
Volumes_Output            vols.dat

PDB files

The coordinates of both complexes have to be provided in PDB fileformat. The corresponding protein atoms in the complexes must have the same names and numbers. Ligands atoms should be specified at the end of the PDB files.

Example

Ligand 1: 

ATOM      1  N   VAL    15     -16.079  -5.086 -26.818  1.00  0.00      A    N
ATOM      2  HT1 VAL    15     -15.166  -5.225 -27.202  1.00  0.00      A    H
ATOM      3  HT2 VAL    15     -16.681  -4.682 -27.507  1.00  0.00      A    H
ATOM      4  HT3 VAL    15     -16.455  -5.959 -26.507  1.00  0.00      A    H
ATOM      5  CA  VAL    15     -15.981  -4.162 -25.660  1.00  0.00      A    C
ATOM      6  HA  VAL    15     -15.336  -4.613 -24.919  1.00  0.00      A    H
ATOM      7  CB  VAL    15     -15.372  -2.809 -26.075  1.00  0.00      A    C
ATOM      8  HB  VAL    15     -15.976  -2.394 -26.869  1.00  0.00      A    H
ATOM      9  CG1 VAL    15     -15.388  -1.835 -24.907  1.00  0.00      A    C
ATOM     10 HG11 VAL    15     -14.785  -2.228 -24.102  1.00  0.00      A    H
ATOM     11 HG12 VAL    15     -16.404  -1.701 -24.564  1.00  0.00      A    H
ATOM     12 HG13 VAL    15     -14.988  -0.884 -25.226  1.00  0.00      A    H
ATOM     13  CG2 VAL    15     -13.958  -2.999 -26.601  1.00  0.00      A    C
ATOM     14 HG21 VAL    15     -13.976  -3.663 -27.452  1.00  0.00      A    H
ATOM     15 HG22 VAL    15     -13.339  -3.426 -25.825  1.00  0.00      A    H
ATOM     16 HG23 VAL    15     -13.553  -2.043 -26.899  1.00  0.00      A    H
ATOM     17  C   VAL    15     -17.350  -3.916 -25.036  1.00  0.00      A    C
ATOM     18  O   VAL    15     -17.551  -4.152 -23.844  1.00  0.00      A    O
ATOM     19  N   LYS    16     -18.288  -3.440 -25.848  1.00  0.00      A    N
ATOM     20  HN  LYS    16     -18.129  -3.247 -26.815  1.00  0.00      A    H
...
ATOM   5506  CZ  PHE   350     -15.849  -0.360   5.961  1.00  0.00      A    C
ATOM   5507  HZ  PHE   350     -14.828  -0.488   5.634  1.00  0.00      A    H
ATOM   5508  CD2 PHE   350     -17.873   0.914   5.988  1.00  0.00      A    C
ATOM   5509  HD2 PHE   350     -18.434   1.784   5.680  1.00  0.00      A    H
ATOM   5510  CE2 PHE   350     -16.567   0.752   5.568  1.00  0.00      A    C
ATOM   5511  HE2 PHE   350     -16.108   1.495   4.932  1.00  0.00      A    H
ATOM   6001  CX1 A62     1      -1.282   3.665   1.884  1.00  1.00      B    C
ATOM   6002  CX2 A62     1      -2.542   3.572   1.263  1.00  1.00      B    C
ATOM   6003  CX3 A62     1      -2.887   2.380   0.608  1.00  1.00      B    C
ATOM   6004  CX4 A62     1      -2.006   1.278   0.577  1.00  1.00      B    C
ATOM   6005  CX5 A62     1      -0.751   1.367   1.240  1.00  1.00      B    C
ATOM   6006  CX6 A62     1      -0.379   2.574   1.858  1.00  1.00      B    C
ATOM   6007  NX1 A62     1      -3.968   2.010  -0.062  1.00  1.00      B    N
ATOM   6008  NX2 A62     1      -3.849   0.868  -0.507  1.00  1.00      B    N
ATOM   6009  CX7 A62     1      -2.682   0.312  -0.169  1.00  1.00      B    C
ATOM   6010  CX8 A62     1      -2.258  -0.985  -0.515  1.00  1.00      B    C
ATOM   6011  CX9 A62     1      -3.237  -1.951  -0.876  1.00  1.00      B    C
ATOM   6012 CX10 A62     1      -2.833  -3.250  -1.218  1.00  1.00      B    C
ATOM   6013  NX3 A62     1      -1.521  -3.554  -1.188  1.00  1.00      B    N
ATOM   6014 CX11 A62     1      -0.544  -2.696  -0.854  1.00  1.00      B    C
ATOM   6015 CX12 A62     1      -0.886  -1.364  -0.518  1.00  1.00      B    C
ATOM   6016  HX5 A62     1      -4.799   2.550  -0.214  1.00  1.00      B    H
ATOM   6017  HX1 A62     1      -1.021   4.512   2.348  1.00  1.00      B    H
ATOM   6018  HX2 A62     1      -3.180   4.342   1.288  1.00  1.00      B    H
ATOM   6019  HX3 A62     1      -0.138   0.578   1.265  1.00  1.00      B    H
ATOM   6020  HX4 A62     1       0.524   2.661   2.280  1.00  1.00      B    H
ATOM   6021  HX6 A62     1      -4.207  -1.706  -0.885  1.00  1.00      B    H
ATOM   6022  HX7 A62     1      -3.509  -3.939  -1.479  1.00  1.00      B    H
ATOM   6023  HX9 A62     1       0.411  -2.993  -0.843  1.00  1.00      B    H
ATOM   6024 HX10 A62     1      -0.175  -0.700  -0.285  1.00  1.00      B    H

Ligand 2: 

ATOM      1  N   VAL    15     -16.079  -5.086 -26.818  1.00  0.00      A    N
ATOM      2  HT1 VAL    15     -15.166  -5.225 -27.202  1.00  0.00      A    H
ATOM      3  HT2 VAL    15     -16.681  -4.682 -27.507  1.00  0.00      A    H
ATOM      4  HT3 VAL    15     -16.455  -5.959 -26.507  1.00  0.00      A    H
ATOM      5  CA  VAL    15     -15.981  -4.162 -25.660  1.00  0.00      A    C
ATOM      6  HA  VAL    15     -15.336  -4.613 -24.919  1.00  0.00      A    H
ATOM      7  CB  VAL    15     -15.372  -2.809 -26.075  1.00  0.00      A    C
ATOM      8  HB  VAL    15     -15.976  -2.394 -26.869  1.00  0.00      A    H
ATOM      9  CG1 VAL    15     -15.388  -1.835 -24.907  1.00  0.00      A    C
ATOM     10 HG11 VAL    15     -14.785  -2.228 -24.102  1.00  0.00      A    H
ATOM     11 HG12 VAL    15     -16.404  -1.701 -24.564  1.00  0.00      A    H
ATOM     12 HG13 VAL    15     -14.988  -0.884 -25.226  1.00  0.00      A    H
ATOM     13  CG2 VAL    15     -13.958  -2.999 -26.601  1.00  0.00      A    C
ATOM     14 HG21 VAL    15     -13.976  -3.663 -27.452  1.00  0.00      A    H
ATOM     15 HG22 VAL    15     -13.339  -3.426 -25.825  1.00  0.00      A    H
ATOM     16 HG23 VAL    15     -13.553  -2.043 -26.899  1.00  0.00      A    H
ATOM     17  C   VAL    15     -17.350  -3.916 -25.036  1.00  0.00      A    C
ATOM     18  O   VAL    15     -17.551  -4.152 -23.844  1.00  0.00      A    O
ATOM     19  N   LYS    16     -18.288  -3.440 -25.848  1.00  0.00      A    N
ATOM     20  HN  LYS    16     -18.129  -3.247 -26.815  1.00  0.00      A    H
...
ATOM   5506  CZ  PHE   350     -15.849  -0.360   5.961  1.00  0.00      A    C
ATOM   5507  HZ  PHE   350     -14.828  -0.488   5.634  1.00  0.00      A    H
ATOM   5508  CD2 PHE   350     -17.873   0.914   5.988  1.00  0.00      A    C
ATOM   5509  HD2 PHE   350     -18.434   1.784   5.680  1.00  0.00      A    H
ATOM   5510  CE2 PHE   350     -16.567   0.752   5.568  1.00  0.00      A    C
ATOM   5511  HE2 PHE   350     -16.108   1.495   4.932  1.00  0.00      A    H
ATOM   6001  CX8 LIG     1      -1.096  -0.730   0.180  1.00  1.00      B    C
ATOM   6002  SX1 LIG     1      -2.713  -1.057  -0.238  1.00  1.00      B    S
ATOM   6003 CX10 LIG     1      -2.345  -2.591  -0.866  1.00  1.00      B    C
ATOM   6004  NX1 LIG     1      -1.032  -2.825  -0.697  1.00  1.00      B    N
ATOM   6005  CX9 LIG     1      -0.370  -1.814  -0.111  1.00  1.00      B    C
ATOM   6006  CX7 LIG     1      -0.613   0.603   0.784  1.00  1.00      B    C
ATOM   6007  CX4 LIG     1      -1.251   1.827   0.127  1.00  1.00      B    C
ATOM   6008  CX5 LIG     1      -0.451   2.645  -0.699  1.00  1.00      B    C
ATOM   6009  C11 LIG     1      -1.026   3.752  -1.360  1.00  1.00      B    C
ATOM   6010  CX1 LIG     1      -2.404   4.031  -1.173  1.00  1.00      B    C
ATOM   6011  CX2 LIG     1      -3.203   3.226  -0.320  1.00  1.00      B    C
ATOM   6012  CX3 LIG     1      -2.618   2.131   0.346  1.00  1.00      B    C
ATOM   6013  NX2 LIG     1      -3.202  -3.436  -1.435  1.00  1.00      B    N
ATOM   6014  HX9 LIG     1      -4.179  -3.203  -1.472  1.00  1.00      B    H
ATOM   6015 HX10 LIG     1      -2.881  -4.296  -1.825  1.00  1.00      B    H
ATOM   6016  HX8 LIG     1       0.607  -1.870   0.097  1.00  1.00      B    H
ATOM   6017  HX6 LIG     1      -0.828   0.613   1.758  1.00  1.00      B    H
ATOM   6018  HX7 LIG     1       0.381   0.668   0.669  1.00  1.00      B    H
ATOM   6019  HX4 LIG     1       0.520   2.443  -0.815  1.00  1.00      B    H
ATOM   6020  HX5 LIG     1      -0.468   4.332  -1.953  1.00  1.00      B    H
ATOM   6021  HX1 LIG     1      -2.819   4.806  -1.650  1.00  1.00      B    H
ATOM   6022  HX2 LIG     1      -4.173   3.435  -0.193  1.00  1.00      B    H
ATOM   6023  HX3 LIG     1      -3.164   1.571   0.970  1.00  1.00      B    H

.

Hydrogen Lists

The protein, ligand 1 and ligand 2 hydrogen lists are necessary. The format of the hlist files if following:

1st column: H or CH3, for single proton or methyl group

2nd column: atom number

3rd column: 1.00

Example

  H     6  1.00
  H     8  1.00
CH3    10  1.00
CH3    11  1.00
CH3    12  1.00
CH3    14  1.00
CH3    15  1.00
CH3    16  1.00
  H    22  1.00
  H    24  1.00
...

SpINPHARMA-hlist

The HList files can be prepared from the PDB file using SpINPHARMA-hlist program. The command is following: 

spinpharma-hlist pdb D off input.pdb > output.hlist

Peaklist file

This file contains information about experimental (or synthetic) peak integrals. The format is following:

1st line: comment line
2nd line: mixing times separated by space(s): tm1 tm2 tm3 ...
3rd line: comment line
4th line: two keywords specifing normalization of the peak volumes

The first keyword value is norm or abs if the input volumes are already normalized(norm) or not (abs). The second keyword controls the normalization scheme:

  • norm_diag for normalization to the corresponding diagonal peak
  • norm_sum for normalization to the sum of all peaks with the same direct dimension assignment
5th line: comment line
6th line and following lines: actual peaks definition
label_F1   label_F2   volume_tm1 flag_tm1    volume_tm2 flag_tm2 ...

Labels specify the ligand and proton group e.g. L1-H1, L2-H12 and LA-HD are correct labels.

Labels must match with the assignment files.

The flag values are:

  • 1 to include the peak in fitting
  • 0 to exclude the
Example
### Mixing times [s]
0.300 0.450 0.600 0.750
################################################################################
norm norm_diag
#
LA-H8  LB-H135  0.0000 0  0.0046 1  0.0096 1  0.0091 1
LA-H34 LB-H135  0.0035 1  0.0026 1  0.0082 1  0.0067 1
LA-H12 LB-H135  0.0031 1  0.0016 1  0.0059 1  0.0055 1
...

Assignment files

Assignment files define the atoms in the PDB file that correspond to the given labels in the peaklist file. Two separate files are necessary for both ligands.

Example

name LA-H8
6019
name LA-H12
6022
6023
name LA-H34
6021  
6024  
name LA-H5
6018

Output files

Quality of fit

The descriptors of the fit quality: Q-factor, R Pearson's correlation coefficient and scaling factor are printed for the all categories of peaks: inter-ligand, intra-ligand(tr-NOEs) and diagonal peaks. The missing values values, for which experimental integrals were not specified, are indicated by -------- symbols.

Q-factor is defined as

$Q = \sqrt{ \sum\limits_{i}^{peaks} \dfrac{(I_{exp,i} - \alpha I_{calc,i})^2}{I_{exp,i}^2} }$

Scaling factor \alpha is defined as

$\alpha = \dfrac{\sum\limits_{i}^{peaks}I_{exp,i}}{\sum\limits_{i}^{peaks}I_{calc,i}}$

Example

L1_filename - L2_filename :  inter_Qf inter_cc inter_scalf , intra_Qf intra_cc intra_scalf , diag_Qf diag_cc diag_scalf
pka_la.pdb - pka_lb.pdb :     0.158415    0.931725    0.369159 ,     --------    --------    -------- ,     --------    --------    --------

Correlation of experimental and calculated integrals

The experimental and calculated values are printed for selected category of peaks. The selection is controlled by configuration file keyword Correlation_Output_Mode .The allowed values are: all, diag, intra and inter

Example

###################################################################
# L1: pka_la.pdb
# L2: pka_lb.pdb
#       LA-H8      LB-H135
  0.00460000   0.00093408
  0.00960000   0.00123089
  0.00910000   0.00146146
...

Calculated integrals

The calculated integrals are saved. The file format is the same as the experimental peaklist.

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