MCCE Program Run and Debug
Commands and Tools
getpdb
Command line tool to download pdb file from PDB
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:
getpdb 1akk
Download with url https://files.rcsb.org/download/1akk.pdb.
Download completed.vdw_pw.py
Update Lennard-Jones potential of step 3 in files head3.lst and energies/*.opp
Syntax:
vdw_pw.py
This program updates Lennard-Jones potential of step 3 in files head3.lst (vdw0 and vdw 1) and 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
vdw_conf2conf.py
Calculate conformer to conformer pairwise vdw (Lennard-Jones potential).
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:
(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: -0.150vdw_bk.py
Calculate conformer to backbone vdw (Lennard-Jones potential).
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:
(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