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MCCE Program Run and Debug

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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:

getpdb 1akk
Download with url https://files.rcsb.org/download/1akk.pdb.
Download completed.

vdw_pw.vdw_bk.py

UpdateCalculate conformer to backbone vdw (Lennard-Jones potentialpotential). of step 3 in files head3.lst and energies/*.opp

Author: Junjun Mao

Syntax:

vdw_pw.vdw_bk.py [-h] [-c cutoff] confID

Compute vdw1 breakdown at conformer level. ThisThe programconformer updatesID Lennard-Jonescan potentialbe 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 stepdisplaying 3 in files head3.lst (vdw0 andconf 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.pairwise

Example:

vdw_pw.(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:

(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_bk.vdw_pw.py

CalculateUpdate conformer to backbone vdw (Lennard-Jones potential)potential of step 3 in files head3.lst and energies/*. opp

Author: Junjun Mao

Syntax:

vdw_bk.vdw_pw.py [-h] [-c cutoff] confID

ComputeThis vdw1program breakdownupdates atLennard-Jones conformerpotential level.of Thestep conformer ID can be found3 in head3.lst.

  • file head3.lst (vdw0 and vdw 1) and
  • files energies/*.opp (vdw column).

positionalA arguments:
copy of confIDhead3.lst Conformerwill IDbe made as in head3.lst

optional arguments:
  -h, --help  show this help messagelst_bak and exit
the  -c cutoff   Cutoff valuecopy of displayingenergies confdirectory will be made as energies_bak. It corrects the some parameter issues in mcce step 3 and offers a chance to rerun vdw pairwisecalculation 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:

(base)vdw_pw.py

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

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