# 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` ---