MCCE Quick Start
Once the path to MCCE4-Alpha/bin is established, MCCE can be run. First, create a directory for the desired protein. We do not recommend mixing different MCCE runs in one directory.
mkdir 4LZT
cd 4LZT
Copy/link your chosen protein into the protein directory. If the desired protein exists on RCSB.org, you can use the tool “getpdb” to download a copy directly from there. For this example, we’ll use 4LZT:
getpdb 4LZT
Now we can run MCCE. The easiest way is with “run_mcce4”, which runs through the first four steps and calculates pKas for each residue of the PDB file, saving them to “pK.out” upon successful completion of the fourth step.
run_mcce4 4lzt.pdb
If MCCE is working properly, your pK.out file should look close to the following text file:
pH pKa/Em n(slope) 1000*chi2 vdw0 vdw1 tors ebkb dsol offset pHpK0 EhEm0 -TS residues total
NTR+A0001_ 6.682 0.973 0.029 -0.00 -0.05 -0.26 0.64 4.31 -0.95 -1.32 0.00 0.00 -1.30 1.08
LYS+A0001_ 9.503 1.006 0.030 -0.03 -0.00 0.00 0.07 0.59 0.29 -0.90 0.00 0.00 -0.02 -0.00
ARG+A0005_ 12.841 0.858 0.061 -0.05 -0.01 0.00 -0.74 0.79 0.00 0.34 0.00 0.23 -0.34 0.23
GLU-A0007_ 3.320 0.965 0.063 -0.00 0.03 -0.20 -1.33 1.26 -0.22 1.43 0.00 0.28 -0.98 0.29
LYS+A0013_ 11.207 0.952 0.042 -0.03 -0.01 0.00 0.20 0.81 0.29 0.81 0.00 0.00 -2.08 0.01
ARG+A0014_ 13.576 0.937 0.038 -0.05 -0.02 0.00 0.05 -0.36 0.00 1.08 0.00 0.36 -0.82 0.23
HIS+A0015_ 6.408 0.986 0.041 -0.03 -0.17 0.00 1.53 1.42 -0.73 -0.57 0.00 0.35 -0.20 1.58
ASP-A0018_ 2.281 0.937 0.114 -0.01 0.04 -0.16 -2.08 1.18 -0.62 2.47 0.00 0.38 -0.81 0.39
TYR-A0020_ 13.497 0.675 0.807 0.00 0.00 0.00 0.46 3.28 -0.37 -3.30 0.00 0.25 -0.21 0.13
ARG+A0021_ 13.259 0.779 0.571 -0.05 -0.02 -0.00 -0.08 0.09 0.00 0.76 0.00 0.24 -0.70 0.24
TYR-A0023_ 10.680 0.864 0.029 0.00 0.00 0.00 -1.22 2.22 -0.37 -0.48 0.00 0.00 -0.15 0.01
LYS+A0033_ 10.700 0.970 0.073 -0.03 -0.01 0.00 0.07 0.70 0.29 0.30 0.00 0.00 -1.26 0.06
GLU-A0035_ 5.586 0.970 0.054 -0.02 0.07 -0.02 -1.30 2.61 -0.22 -0.84 0.00 0.20 -0.28 0.19
ARG+A0045_ 13.282 0.679 2.103 -0.05 -0.00 0.00 0.18 -0.25 0.00 0.78 0.00 0.44 -0.67 0.41
ASP-A0048_ 1.567 0.966 0.024 -0.01 0.03 -0.25 -2.58 3.38 -0.62 3.18 0.00 0.12 -3.14 0.12
ASP-A0052_ 2.448 0.958 0.034 -0.01 0.07 -0.09 -1.23 2.32 -0.62 2.30 0.00 0.52 -2.29 0.97
TYR-A0053_ >14.0 0.00 0.00 0.00 -1.69 4.65 -0.37 -3.80 0.00 0.00 7.32 6.12
ARG+A0061_ 13.749 0.803 0.003 -0.07 -0.02 -0.00 0.84 0.28 0.00 1.25 0.00 0.39 -2.26 0.40
ASP-A0066_ 0.019 0.994 0.147 -0.01 0.08 -0.16 -5.86 7.51 -0.62 4.73 0.00 0.13 -7.46 -1.66
ARG+A0068_ 13.767 0.585 1.272 -0.03 -0.01 0.00 0.34 -0.38 0.00 1.27 0.00 0.00 156.81 158.00
ARG+A0073_ 13.069 0.876 0.424 -0.05 -0.01 0.00 -0.15 -0.06 0.00 0.57 0.00 0.40 -0.31 0.38
ASP-A0087_ 2.120 0.971 0.100 -0.01 0.05 -0.21 -2.02 1.34 -0.62 2.63 0.00 0.32 -1.16 0.32
LYS+A0096_ 10.696 0.782 0.462 -0.04 -0.03 0.00 -1.65 1.42 0.29 0.30 0.00 0.00 -0.27 0.02
LYS+A0097_ 10.881 0.880 0.061 -0.03 -0.01 0.00 -0.28 0.16 0.29 0.48 0.00 0.00 -0.62 -0.01
ASP-A0101_ 4.249 1.018 0.013 -0.00 0.03 -0.11 0.08 1.32 -0.62 0.50 0.00 0.57 -1.18 0.57
ARG+A0112_ 12.855 0.897 0.004 -0.06 -0.02 0.00 -0.23 0.77 0.00 0.35 0.00 0.47 -0.74 0.54
ARG+A0114_ 13.286 0.945 0.004 -0.07 -0.01 0.00 -0.07 -0.25 0.00 0.79 0.00 0.35 -0.39 0.36
LYS+A0116_ 9.559 0.952 0.068 -0.04 -0.00 0.00 0.11 0.48 0.29 -0.84 0.00 0.00 0.01 0.02
ASP-A0119_ 3.692 0.976 0.020 -0.01 0.05 -0.25 -1.15 2.15 -0.62 1.06 0.00 0.07 -1.23 0.07
ARG+A0125_ 13.176 0.906 0.020 -0.06 -0.01 0.00 0.40 -0.12 0.00 0.68 0.00 0.38 -0.88 0.38
ARG+A0128_ 13.608 0.929 0.053 -0.04 -0.00 0.00 0.07 -0.80 0.00 1.11 0.00 0.42 -0.35 0.42
CTR-A0129_ 2.570 0.899 0.077 0.01 0.06 -0.11 -0.04 1.67 0.00 1.18 0.00 0.52 -2.77 0.54
Other files are created by MCCE in the process of creating “pK.out”. Learn about these output files here. Learn more about the four individual steps that comprise run_mcce4 here.
How do I run MCCE on multiple PDB files at once?
How do I know if the run processed correctly?
How do I interpret MCCE’s Output Files?