# MCCE Commands # MCCE Program Run and Debug ### Commands and Tools --- #### getpdb *Command line tool to download pdb file from PDB* **Author:** Yanjun Wang **Syntax:** `getpdb pdbID [file]` This program gets a pdb file from Protein Data Bank, and saves to a file with its PDB name or a user named file. **Example:** ```bash getpdb 1akk Download with url https://files.rcsb.org/download/1akk.pdb. Download completed. ``` --- #### vdw\_bk.py *Calculate conformer to backbone vdw (Lennard-Jones potential). * **Author:** Junjun Mao **Syntax:** `vdw_bk.py [-h] [-c cutoff] confID` Compute vdw1 breakdown at conformer level. The conformer ID can be found in head3.lst. positional arguments: confID Conformer ID as in head3.lst optional arguments: -h, --help show this help message and exit -c cutoff Cutoff value of displaying conf vdw pairwise **Example:** ```bash (base) jmao@Jupiter:~/projects/1akk$ vdw_bk.py GLU-1A0090_005 -c 0.1 LEUBKA0064_000 -0.104 METBKA0065_000 -0.499 LEUBKA0068_000 -0.825 GLUBKA0069_000 -0.758 ILEBKA0085_000 -0.571 LYSBKA0086_000 -0.990 LYSBKA0087_000 -1.005 LYSBKA0088_000 -1.011 THRBKA0089_000 -0.876 GLUBKA0090_000 1.424 ARGBKA0091_000 2.383 GLUBKA0092_000 -0.204 ASPBKA0093_000 -0.113 LEUBKA0094_000 -0.120 Total -3.616 ``` --- #### vdw\_conf2conf.py *Calculate conformer to conformer pairwise vdw (Lennard-Jones potential).* **Author:** Junjun Mao **Syntax:** `vdw_conf2conf.py [-h] [-c cutoff] [-v] confID confID` Compute detailed conformer to conformer vdw. positional arguments: confID Conformer ID as in head3.lst, two IDs required. optional arguments: -h, --help show this help message and exit -c cutoff Cutoff value of displaying atom to atom vdw -v Turn on verbose mode, displaying more details This program calculates Lennard-Jones potential between a conformer pair, which should be consistent with the number in opp file under energies directory. The pair could be self to self, which is vdw0 term in head3.lst. The programs reports atom to atom interaction and atom connectivity as well. The conformer ID can be found in head3.lst. **Example:** ```bash (base) jmao@Jupiter:~/projects/1akk$ vdw_conf2conf.py GLU-1A0090_005 THR01A0089_002 -c 0.01 -v ATOM1 ATOM2 vdw dist cnct r1 e1 r2 e2 R_sum E_par CB GLU0090A005 -> CB THR0089A002: -0.024 5.446 none 1.9080 0.1094 1.9080 0.1094 3.8160 0.1094 CB GLU0090A005 -> OG1THR0089A002: -0.010 6.361 none 1.9080 0.1094 1.7210 0.2104 3.6290 0.1517 CG GLU0090A005 -> CB THR0089A002: -0.016 5.883 none 1.9080 0.1094 1.9080 0.1094 3.8160 0.1094 GLU-1A0090_005 - THR01A0089_002: -0.150 ``` --- #### vdw\_pw.py *Update Lennard-Jones potential of step 3 in files head3.lst and energies/\*.opp* **Author:** Junjun Mao **Syntax:** `vdw_pw.py` This program updates Lennard-Jones potential of step 3 in - file head3.lst (vdw0 and vdw 1) and - files energies/\*.opp (vdw column). A copy of head3.lst will be made as head3.lst\_bak and the copy of energies directory will be made as energies\_bak. It corrects the some parameter issues in mcce step 3 and offers a chance to rerun vdw calculation without running PB solver again. Also it checks the possible inconsistancy in parameter files and comes with two other tools: vdw\_conf2conf.py and vdw\_bk.py to inspect the vdw interaction clashes. **Example:** `vdw_pw.py` --- # MCCE Data Analysis ### MCCE data analysis tools #### fitpka.py *Fit the titration curve of an ionizable residue.* **Syntax:** `fitpka.py [-h] RES [RES ...]` Fit a titration of charged residues positional arguments: RES Charged residue names to plot, as in sum\_crg.out or pK.out optional arguments: -h, --help show this help message and exit
**Required input file** - sum\_crg.out **Example:** Find the residue IDs: ``` $ cat sum_crg.out pH 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 NTR+A0001_ 1.00 1.00 1.00 1.00 0.99 0.96 0.70 0.20 0.03 0.00 0.00 0.00 0.00 0.00 0.00 LYS+A0001_ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.97 0.78 0.27 0.04 0.00 0.00 0.00 ARG+A0005_ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.97 0.80 0.38 0.08 GLU-A0007_ -0.00 -0.01 -0.07 -0.38 -0.84 -0.98 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 LYS+A0013_ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.99 0.95 0.67 0.19 0.03 0.00 ARG+A0014_ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.99 0.94 0.66 0.19 HIS+A0015_ 1.00 1.00 1.00 1.00 1.00 0.98 0.83 0.36 0.06 0.01 0.00 0.00 0.00 0.00 0.00 ASP-A0018_ -0.01 -0.10 -0.49 -0.89 -0.99 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 TYR-A0020_ -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.01 -0.03 -0.09 -0.32 -0.73 ARG+A0021_ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.99 0.91 0.59 0.22 TYR-A0023_ -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.01 -0.06 -0.32 -0.76 -0.96 -0.99 -1.00 LYS+A0033_ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.97 0.78 0.27 0.05 0.01 0.00 GLU-A0035_ -0.00 -0.00 -0.01 -0.03 -0.12 -0.46 -0.88 -0.98 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 ARG+A0045_ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.99 0.91 0.56 0.21 ASP-A0048_ -0.03 -0.21 -0.69 -0.95 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 ASP-A0052_ -0.00 -0.01 -0.07 -0.44 -0.84 -0.95 -0.99 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 TYR-A0053_ -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 ARG+A0061_ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.98 0.90 0.57 ASP-A0066_ -0.03 -0.20 -0.68 -0.93 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 ARG+A0068_ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.99 0.95 0.76 0.34 ARG+A0073_ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.98 0.85 0.39 0.09 ASP-A0087_ -0.01 -0.08 -0.44 -0.88 -0.98 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 LYS+A0096_ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.96 0.76 0.33 0.08 0.02 0.01 LYS+A0097_ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.98 0.85 0.40 0.08 0.01 0.00 ASP-A0101_ -0.00 -0.00 -0.01 -0.09 -0.51 -0.91 -0.99 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 ARG+A0112_ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.98 0.87 0.43 0.09 ARG+A0114_ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.99 0.94 0.63 0.17 LYS+A0116_ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.97 0.75 0.27 0.05 0.01 0.00 0.00 ASP-A0119_ -0.00 -0.00 -0.03 -0.19 -0.71 -0.96 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 ARG+A0125_ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.99 0.90 0.55 0.13 ARG+A0128_ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.99 0.97 0.79 0.31 CTR-A0129_ -0.00 -0.04 -0.29 -0.75 -0.96 -0.99 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 ---------- Net_Charge 18.93 18.34 16.22 13.47 11.05 9.70 8.68 7.57 7.01 6.38 4.53 1.82 -0.64 -4.61 -9.32 Protons 18.93 18.34 16.22 13.47 11.05 9.70 8.68 7.57 7.01 6.38 4.53 1.82 -0.64 -4.61 -9.32 Electrons 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ``` Fit the titration curves of residue GLU-A0035\_ and ASP-A0052\_: `fitpka.py GLU-A0035_ ASP-A0052_` [![fitpks_example.png](https://mccewiki.levich.net/uploads/images/gallery/2023-03/scaled-1680-/fitpks-example.png)](https://mccewiki.levich.net/uploads/images/gallery/2023-03/fitpks-example.png) --- #### mfe.py *Analyze ionization free energy of a residue. It tells you why a residue has that pKa and what factors played a role.* **Syntax**
`mfe.py [-h] [-p pH/Eh] [-x TS_correction] [-c cutoff] residue`
- residue: residue ID as in pK.out - pH/Eh: pH value at which ionization energy is calculated. Default is the pKa (midpoint) where dG = 0. - cut\_off: Report only pairwise interaction bigger than this value. - TS\_correction: "t" to include entropy in G, "f" not to include, "r" (default) will look for run.prm. If entropy correction was turned on in step 4, mfe should not include this term as entropy has been "removed". **Required files:** - run.prm - head3.lst - extra.tpl for scaling factors that are not equal to 1. - energies/\*.opp for pairwise interactions **Example:** Check titration result in pKa.out: ``` cat pK.out ... ASP-A0052_ 3.152 ... ``` ASP-A0052\_ is the residue\_ID. Its calculated pKa is 3.152. At this point, the free energy of reaction from ASP neutral to ASP ionized should be close to 0. Run ``` $ mfe.py ASP-A0052_ -c 0.1 Residue ASP-A0052_ pKa/Em=3.152 ================================= Terms pH meV Kcal --------------------------------- vdw0 -0.01 -0.85 -0.02 vdw1 0.00 0.23 0.01 tors -0.10 -5.86 -0.14 ebkb -1.27 -73.44 -1.73 dsol 1.99 115.38 2.71 offset -0.62 -36.17 -0.85 pH&pK0 1.60 92.75 2.18 Eh&Em0 0.00 0.00 0.00 -TS 0.00 0.00 0.00 residues -1.36 -79.01 -1.86 ********************************* TOTAL 0.22 13.04 0.31 sum_crg ********************************* ASNA0044_ -0.46 -26.92 -0.63 0.00 ARGA0045_ -0.11 -6.36 -0.15 1.00 ASNA0046_ -0.19 -11.09 -0.26 0.00 ASPA0048_ 0.50 28.96 0.68 -0.96 SERA0050_ 0.13 7.28 0.17 0.00 GLNA0057_ 0.22 12.78 0.30 0.00 ASNA0059_ -0.99 -57.18 -1.34 0.00 ARGA0061_ -0.26 -15.37 -0.36 1.00 ASPA0066_ 0.27 15.72 0.37 -0.94 ARGA0112_ -0.19 -11.11 -0.26 1.00 ARGA0114_ -0.10 -5.86 -0.14 1.00 ================================= ``` You can do mfe calculation at pH other than mid-point. # MCCE Tools List of miscellaneous tools MCCE offers for your research and convenience. Most of these tools support "-h" flags for additional information and use cases. Some of these tools are intended for *pre-run* analysis, and some are intended for **post-run** analysis. Pre-run tools will be *italicized*, and are found in the MCCE\_bin of a [MCCE4-Alpha directory](https://github.com/GunnerLab/MCCE4-Alpha). Post-run tools will be **bolded**, and are found in [MCCE4-Tools](https://github.com/GunnerLab/MCCE4-Tools), a separate git directory. ### **cif2pdb (MCCE4-Tools)** usage: cif\_to\_pdb file.cif \[file.pdb\] Converts a .cif file to .pdb format. ### **clear\_mcce\_folder (MCCE4-Tools)** Deletes all MCCE outputs from the present working directory, except: run.prm, the original PDB file, prot.pdb, and any non-MCCE files. ### detect\_hbonds.py Detect H-bonds in a PDB file, with the option to include BK (backbone) atoms. hbonds\_pdb\_collection uses this function on a collection of PDB files. usage: detect\_hbonds.py \[-h\] \[--include\_bk\] \[--no\_empty\_files\] \[--out\_dir OUT\_DIR\] \[inpdb\] ### extract\_md\_frames Extracts the trajectory's frames with the given indices into PDB files. Requires the MDAnalysis package. ### filesdiff Obtain the column difference between two MCCE files or the differences of all files in two MCCE output folders. Use the "-threshold" flag to output absolute differences beyond a given value (0 is default). Applicable to the following MCCE files: 'all\_pK.out', 'all\_sum\_crg.out', 'entropy.out', 'fort.38', 'head3.lst', 'pK.out', 'residues\_stats.txt', 'sum\_crg.out', 'vdw0.lst'. ### fix\_psf\_mdanalysis Provides a reformatted PSF file if "MDAnalysis" fails to parse the given PSF. Requires the "MDAnalysis" and "parmed" packages. ### getpdb Downloads one or more (bioassembly) PDB files from the RCSB Protein Databank. For example, to download triclinic hew lysozyme (4LZT), one could type in usage: getpdb \[RCSB protein code\] ### glossary Gives detailed information regarding the various parameters of run.prm, where MCCE looks to handle more granular customization. You can search for specific parameters by with a given (case-sensitive) prefix string. For example, "glossary T" will return all parameters starting with T, like "TITR\_TYPE". The command "glossary --print" also prints the entire glossary. ### hbonds\_pdb\_collection Detects Hydrogen bonds, using detect\_hbonds.py, over a collection of PDB files, in the step2\_out.pdb format. ASK HOW TO USE THIS usage: hbonds\_pdb\_collection \[-h\] \[-input\_dir INPUT\_DIR\] \[-output\_dir OUTPUT\_DIR\] \[--include\_bk\] \[--no\_empty\_files\] ### mcce\_stat Prints a table to keep track of progressing MCCE runs. Four "sentinel" files are looked for, to signify completion of each of the four basic steps of MCCE: step1\_out.pdb, step2\_out.pdb, head3.lst, and pK.out. pK.out signifies completion of step 4, so if a book.txt exists for a protein when mcce\_stat is run, that protein will receive a "c" in book.txt to signify completion. We recommend using mcce\_stat with p\_batch. ### ms\_hbond\_percentages.py Creates a table displaying all Hydrogen bond connections across microstate PDBs, and their percentages. Defaults to the local directory named pdb\_output\_mc\_hbonds. usage: ms\_hbond\_percentages.py \[-h\] \[dir\] ### ms\_top2pdbs Stands for Tautomeric Charge MicroStates. Outputs: the top N tautomeric charge microstates, along with related properties energy (E), net charge (sum\_crg), count, and occupancy (occ); a summary file identifying ionizble residues with non-canonical charge, and which residues that do not change charge over the topN set; and the top N files of each charge state in PDB and PQR format. By default, charge microstates are retrieved at pH 7, and the number of most favorable charge microstates (N\_TOP) returned is five. usage: ms\_top2pdbs inputpdb\_filepath \[-ph PH\] \[-n\_top N\_TOP\] ### *p\_batch (MCCE\_bin)* Starts multiple protein runs at once, using the same set of instructions, and creates a book.txt file to manage their completion status. p\_batch accepts a directory containing protein files, and (optionally) a shell script given custom instructions. If a shell script is not provided, a default one will be created, and may be edited to the user's preference. If a file named "run.prm.custom" is in the present working directory at runtime, the file will be read to override the default run.prm instructions. p\_batch creates a run directory for each protein file, and begins running MCCE for each one. Files will be created for their respective directories as each step is completed. Use mcce\_stat to check how each run is progressing. To stop a run in progress, delete the files or directory associated with the run. ### *p\_info (MCCE\_bin)* Gives a high-level summary of characteristics of a PDB file, including residue, chain, and ligand counts, as well as other aspects of a PDB changed during step 1 of MCCE, including how residues are named. If step 1 has not been run on the PDB file at runtime, p\_info will automatically run step 1 before continuing as normal. ### **pdbs2pse (MCCE4-Tools)** usage: pdbs2pse file1.pdb file2.pdb ... \[--pse\_name <output\_name>\] Converts one or more PDB files into a single PyMOL session file (.pse). The session file contains all the loaded PDB structures as separate objects. The user can specify an optional output name for the .pse file, or it will default to the name of the last input PDB file. ### **postrun (MCCE4-Tools)** usage (in a directory with sum\_crg.out, pK.out files): postrun \[-h\] \[-run\_dir RUN\_DIR\] \[--is\_benchmark\] postrun provides basic diagnostics on sum\_crg.out and pk.out files, after a run is completed. postrun looks for non-canonically charged residues, residues without curve fit or a chi-squared above 3, and residues that are out-of-bounds. The problem residues are outputted to the terminal and saved to a "postrun.bad" file. If there are no problem residues, a "postrun.ok" file is created instead. postrun can be run on a directory of completed protein runs, with the flag "-run\_dir". ### txt\_to\_csv A quick script that copies a given file into a .csv format. The source file does not need to be a .txt file. Recommended to use with spreadsheets.