MCCE tools reference¶

Page last updated on: 2020-12-30

Improving and helping runs¶

step by step mcce run scripts¶

MCCE involves 4 main steps:

Step 1: Convert raw PDB file to MCCE PDB file, reformat terminal residues, and strip off surface water and ions.
Step 2: Make side chain conformers, including rotamers and ionization conformers.
Step 3: Compute self-energy of conformers and pairwise energy lookup table.
Step 4: Monte Carlo sampling to evaluate favorable side chain position and ionization at various conditions.

While the control of these 4 steps is fully configured in run.prm and executed by mcce command, the 4 steps can be carried out by python wrapper scripts without configuring run.prm.

Step 1: prepare structure¶

usage: step1.py [-h] [--norun] [--noter] [-e /path/to/mcce] [-u Key=Value]
                [-d epsilon] [--dry]
                pdb

Run mcce step 1, premcce to format PDB file to MCCE PDB format.

positional arguments:
  pdb

optional arguments:
  -h, --help        show this help message and exit
  --norun           Create run.prm but do not run step 1
  --noter           Do not label terminal residues (for making ftpl).
  -e /path/to/mcce  mcce executable location, default to "mcce"
  -u Key=Value      User customized variables
  -d epsilon        protein dielectric constant for delphi, default to 4.0
  --dry             Delete all water molecules.

Step 2: make conformers¶

usage: step2.py [-h] [--norun] [-d epsilon] [-e /path/to/mcce] [-u Key=Value]
                [-l level]

Run mcce step 2, make side chain conformers from step1_out.pdb.

optional arguments:
  -h, --help        show this help message and exit
  --norun           Create run.prm but do not run step 2
  -d epsilon        dielectric constant for optimizing conformers
  -e /path/to/mcce  mcce executable location, default to "mcce"
  -u Key=Value      User customized variables
  -l level          conformer level 1: quick, 2: medium, 3: comprehensive

Step 3: energy calculation¶

usage: step3.py [-h] [-c start end] [-d epsilon] [-e /path/to/mcce]
                [-f tmp folder] [-p processes] [-r] [-u Key=Value]
                [-x /path/to/delphi] [--norun]

Run mcce step 3, energy calculations, with multiple threads.

optional arguments:
  -h, --help          show this help message and exit
  -c start end        starting and ending conformer, default to 1 and 9999
  -d epsilon          protein dielectric constant for delphi, default to 4.0
  -e /path/to/mcce    mcce executable location, default to "mcce"
  -f tmp folder       delphi temporary folder, default to /tmp
  -p processes        run mcce with number of processes, default to 1
  -r                  refresh opp files and head3.lst without running delphi
  -u Key=Value        User customized variables
  -x /path/to/delphi  delphi executable location, default to "delphi"
  --norun             Create run.prm but do not run step 3

step3.py is able to run in multiple threads.

Step 4: Monte Carlo sampling¶

usage: step4.py [-h] [--norun] [-i initial ph/eh] [-d interval] [-n steps]
                [--xts] [--ms] [-e /path/to/mcce] [-t ph or eh] [-u Key=Value]

Run mcce step 4, Monte Carlo sampling to simulate a titration.

optional arguments:
  -h, --help        show this help message and exit
  --norun           Create run.prm but do not run step 4
  -i initial ph/eh  Initial pH/Eh of titration
  -d interval       titration interval in pJ or mV
  -n steps          number of steps of titration
  --xts             Enable entropy correction, default is false
  --ms              Enable microstate output
  -e /path/to/mcce  mcce executable location, default to "mcce"
  -t ph or eh       titration type, pH or Eh
  -u Key=Value      User customized variables

Step 5: titration fitting¶

Step 5 is optional. It writes net charge of each residue in sum_crg2.out and fits the titration curve in pK2.out.

usage: step5.py [-h]

Run mcce step 5, generate net charge, fit titration curve.

optional arguments:
  -h, --help  show this help message and exit

Step 6: hydrogen bond¶

Step 6 is for hydrogen bond network analysis. It requires step 4 to output microstates.

usage: step6.py [-h] [--norun] [-e /path/to/mcce] [-u Key=Value]

Run step 6, hydrogen bond analysis, requires microstate output from step 4.

optional arguments:
  -h, --help        show this help message and exit
  --norun           Create run.prm but do not run step 6
  -e /path/to/mcce  mcce executable location, default to "mcce"
  -u Key=Value      User customized variables

Example:

step4.py --ms
step6.py

Combine first 4 steps¶

The first 4 steps are essential steps.

#!/bin/bash
step1.py input.pdb
step2.py
step3.py
step4.py

energies.py¶

Run step3 with multiple threads.

Syntax:

energies.py [-h] [-p processes] [-r] [-c start end] [-e /path/to/mcce]

Optional arguments:

Argument	Description
-h, --help	show this help message and exit
-p processes	run mcce with number of processes, default to 1
-r	refresh opp files and head3.lst without running delphi
-c start end	starting and ending conformer, default to 1 and 9999
-e /path/to/mcce	mcce executable location, default to "mcce"

Examples:

energies.py -p 6

This command runs step 3 in 6 threads.

energies.py -r

This command runs step 3 just to refresh head3.lst and vdw energy.

energies.py -c 1 100 -p 4

This command calculates conformer from 1 to 100 in 5 threads.

Note

After this command, the lines:

1       delphi start conformer number, 0 based            (PBE_START)
99999   delphi end conformer number, self included        (PBE_END)

in run.prm file might be altered.

getpdb¶

Download a pdb file by its PDB ID.

Syntax:

getpbd pdbid [saved name]

Example:

getpdb 1akk
Inquiring the remote file 1AKK.pdb ...
Saving as 1AKK.pdb ...
Download completed.

Or

getpdb 1akk prot.pdb
Inquiring the remote file 1AKK.pdb ...
Saving as prot.pdb ...
Download completed.

to save as specified name.

translate_step2.py¶

Translate old atom names in step2_out to new PDB v3 names.

Syntax:

translate_step2.py step2_out.pdb

Hydrogen names in PDB v3 are significantly different from PDB v2. Due to the randomness in step 2, it is sometimes desired to preserve step2_out.pdb. This tool translates the names so that step2_out.pdb so that it can be used by new mcce.

This program prints the translated content on screen. So the user is responsible to make backup of the step2_out.pdb file and redirect the outcome to a new step2_out.pdb.

Example:

cp step2_out.pdb step2_out.pdb.bak
translate_step2.py step2_out.pdb.bak > step2_out.pdb

Result Analysis¶

fitpka.py¶

Fit the titration curve of an ionizable residue.

Syntax:

$ fitpka.py -h 
usage: fitpka.py [-h] RES [RES ...]

Fit a titration of charged residues

positional arguments:
  RES         Charged residue names to plot, as in sum_crg.out

optional arguments:
  -h, --help  show this help message and exit

Required input file

sum_crg.out

Example:

$ 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  0.99  0.92  0.55  0.12  0.01  0.00  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  0.79  0.28  0.05  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  0.96  0.79  0.36  0.07
GLU-A0007_ -0.00 -0.01 -0.08 -0.40 -0.85 -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  0.67  0.20
HIS+A0015_  1.00  1.00  1.00  1.00  1.00  0.98  0.86  0.40  0.06  0.01  0.00  0.00  0.00  0.00  0.00
ASP-A0018_ -0.01 -0.10 -0.50 -0.88 -0.98 -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 -0.04 -0.09 -0.31 -0.69
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  0.60  0.21
TYR-A0023_ -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.00 -0.01 -0.07 -0.35 -0.79 -0.97 -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  0.28  0.04  0.01  0.00
GLU-A0035_ -0.00 -0.00 -0.00 -0.03 -0.12 -0.42 -0.86 -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  0.98  0.86  0.44  0.15
ASP-A0048_ -0.03 -0.24 -0.74 -0.95 -0.99 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00 -1.00
ASP-A0052_ -0.00 -0.00 -0.07 -0.34 -0.79 -0.96 -1.00 -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  0.89  0.56
ASP-A0066_ -0.00 -0.00 -0.38 -1.00 -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  0.94  0.74  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  0.83  0.37  0.08
ASP-A0087_ -0.01 -0.09 -0.46 -0.88 -0.99 -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  0.97  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  0.84  0.41  0.07  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  0.99  0.88  0.47  0.11
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  0.93  0.64  0.16
LYS+A0116_  1.00  1.00  1.00  1.00  1.00  1.00  1.00  1.00  0.97  0.76  0.28  0.05  0.01  0.00  0.00
ASP-A0119_ -0.00 -0.00 -0.03 -0.20 -0.72 -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  0.54  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  1.00  0.96  0.78  0.29
CTR-A0129_ -0.00 -0.04 -0.28 -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 18.95 18.51 16.44 13.45 11.02  9.32  8.13  7.43  6.98  6.40  4.52  1.80 -0.72 -4.73 -9.38
Protons    18.95 18.51 16.44 13.45 11.02  9.32  8.13  7.43  6.98  6.40  4.52  1.80 -0.72 -4.73 -9.38
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

Find the residue ID in sum_carg.out, then fit the titration curve:

fitpka.py ASP-A0066_

state.py¶

Analyze how a microstate energy is composed.

Syntax:

state.py

Required files:

run.prm
head3.lst
extra.tpl for scaling factors that are not equal to 1.
energies/*.opp for pairwise interactions
microstate file named "states"

The microstate file is in a fixed format. The first line is like:

T=298.15, ph=7.0, eh=0.0

It specifies the the environment variables which affects the energy calculation. Variables are separated by ", ". The variable names are not case sensitive.

T: Temperature. Room temperature is 298.15 K
ph: pH value.
eh: Eh value, the electric potential for potential titration.

The rest of the lines are microstates. One line per state. Each line consists the index number of conformers (0 based). Numbers can be separated by either comma or space.

Example:

Make a states file:

Run

state.py

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-A0044_        3.947
...

ASP-A0052 is the residue_ID. Its calculated pKa is 2.275. At this point, the free energy of reaction from ASP neutral to ASP ionized should be close to 0.

Run

$ mfe.py -c 0.01 ASP-A0044_ 
Residue ASP-A0044_ pKa/Em=3.947
=================================
Terms          pH     meV    Kcal
---------------------------------
vdw0        -0.00   -0.27   -0.01
vdw1        -0.01   -0.59   -0.01
tors        -0.15   -8.63   -0.20
ebkb        -0.67  -38.66   -0.91
dsol         0.26   15.35    0.36
offset      -0.62  -36.17   -0.85
pH&pK0       0.80   46.61    1.10
Eh&Em0       0.00    0.00    0.00
-TS          0.58   33.46    0.79
residues    -0.19  -11.14   -0.26
*********************************
TOTAL       -0.00   -0.05   -0.00  sum_crg
*********************************
NTRA0003_   -0.03   -1.66   -0.04    1.00
ASPA0022_    0.02    0.95    0.02   -0.86
ASNA0023_   -0.01   -0.68   -0.02    0.00
LYSA0027_   -0.01   -0.77   -0.02    1.00
LYSA0039_   -0.14   -8.23   -0.19    1.00
ASNA0041_   -0.01   -0.62   -0.01    0.00
LYSA0049_   -0.04   -2.10   -0.05    1.00
ASPA0054_    0.01    0.69    0.02   -0.95
GLUA0073_    0.01    0.79    0.02   -0.99
ASPA0075_    0.05    2.85    0.07   -1.00
TYRA0078_    0.02    1.05    0.02   -0.00
SERA0080_    0.02    1.19    0.03    0.00
ARGA0083_   -0.04   -2.51   -0.06    1.00
ARGA0087_   -0.03   -1.49   -0.04    1.00
HISA0102_   -0.02   -1.02   -0.02    1.00
=================================

You can do mfe calculation at pH other than mid-point.

mfe_all.py¶

Perform mfe analysis on all ionizable residues.

Syntax

mfe_all.py [-h] [-p pH/Eh] [-x TS_correction] [-f format] [-o filename]

pH/Eh: pH value at which ionization energy is calculated. Default is the pKa (midpoint) where dG = 0.
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".
format: output file format, xlsx, csv, or html. The default is excel format xlsx.
filename: output file name. The default is mfe_all.[ext]

Required files:

run.prm
head3.lst
extra.tpl for scaling factors that are not equal to 1.
energies/*.opp for pairwise interactions

Example:

mfe_all.py -f html
MFE output saved in file mfe_all.html

mostocc.py¶

Extract most occupied conformer from fort.38 and make a pdb file.

Syntax

mostocc.py pH

pH is the exact pH in the first line of fort.38 file. It indicates which pH to use for occupancy, as occupancy is pH dependent.

Required files:

fort.38
step2_out.pdb

Example:

mostocc.py 7.0

sanity.py¶

Quick check on the charge state of ionizable residues abd report unusual charge.

Syntax

sanity.py

Required files:

run.prm
sum_crg.out

Example:

$ sanity.py 
TYR-A0013_: charge  0.00 expected near -1.0 at pH=12.0
HIS+A0018_: charge  0.00 expected near  1.0 at pH= 0.0
TYR-A0024_: charge  0.00 expected near -1.0 at pH=12.0
LYS+A0062_: charge  0.55 expected near  0.0 at pH=13.0
GLU-A0073_: charge -0.74 expected near  0.0 at pH= 2.0
ASP-A0075_: charge -1.00 expected near  0.0 at pH= 0.0
TYR-A0078_: charge  0.00 expected near -1.0 at pH=12.0
TYR-A0090_: charge -0.09 expected near -1.0 at pH=12.0
ASP-A0093_: charge -0.83 expected near  0.0 at pH= 1.0
TYR-A0097_: charge -0.17 expected near -1.0 at pH=12.0
TYR-A0103_: charge  0.00 expected near -1.0 at pH=12.0

Parameter file preparation¶

pdb2ftpl.py¶

This tool converts a pdb file to a ftpl template.

Syntax

usage: pdb2ftpl.py [-h] [-d] [-c conformer type] pdbfile

Create a ftpl template file from a cofactor PDB file. The atoms in the input
files are considered as one molecule.

positional arguments:
  pdbfile

optional arguments:
  -h, --help         show this help message and exit
  -d                 Ignore CONNECT, use distance to determine bond
  -c conformer type  Specify a 2-character conformer type ID, default 01

mol2_charge.py¶

Apply mol2 charge to a conformer in ftpl template. The mol2 file doesn't need to have the matching atom names, as long as the element names are correct.

Syntax

$ mol2_charge.py -h
usage: mol2_charge.py [-h] -m mol2 -c conf [--show] ftpl

Apply mol2 charge to a conformer in ftpl template. The mol2 file doesn't need
to have the matching atom names, as long as the element names are correct.

positional arguments:
  ftpl

optional arguments:
  -h, --help  show this help message and exit
  -m mol2     mol2 file with charge
  -c conf     Conformer ID in conformer list to be matched.
  --show      Show atom name matching, default false.

Example:

If I have a ftpl file T4Y.tpl and a mol2 file 27c-p.mol2 with atom charge.

$ mol2_charge.py -m 27c-p.mol2 T4Y.ftpl -c T4Y01 --show
=================
 ftpl  ---  mol2
=================
" N1 " --- "N4"
" C4 " --- "C14"
" C5 " --- "C13"
" C6 " --- "C12"
" C7 " --- "C11"
" C8 " --- "C7"
" C10" --- "C5"
" C13" --- "C2"
" N  " --- "N8"
" C  " --- "C18"
" O  " --- "O3"
" C1 " --- "C17"
" C11" --- "C10"
" C12" --- "C9"
" C14" --- "C1"
" C2 " --- "C16"
" C3 " --- "C15"
" C9 " --- "C6"
" H5 " --- "H35"
" H6 " --- "H34"
" H8 " --- "H32"
" H7 " --- "H33"
" H9 " --- "H26"
" H10" --- "H27"
" H13" --- "H22"
" H14" --- "H23"
" H1 " --- "H38"
" H  " --- "H39"
" H2 " --- "H40"
" H15" --- "H30"
" H16" --- "H31"
" H18" --- "H28"
" H17" --- "H29"
" H22" --- "H19"
" H19" --- "H20"
" H20" --- "H21"
" H3 " --- "H37"
" H4 " --- "H36"
" H11" --- "H24"
" H12" --- "H25"
=================
CHARGE, T4Y01, " N1 ":   -0.45
CHARGE, T4Y01, " C4 ":   -0.14
CHARGE, T4Y01, " C5 ":   -0.11
CHARGE, T4Y01, " C6 ":   -0.09
CHARGE, T4Y01, " C7 ":    0.22
CHARGE, T4Y01, " C8 ":    0.17
CHARGE, T4Y01, " C10":    0.09
CHARGE, T4Y01, " C13":    0.66
CHARGE, T4Y01, " N  ":   -0.75
CHARGE, T4Y01, " C  ":   -0.05
CHARGE, T4Y01, " O  ":   -0.61
CHARGE, T4Y01, " C1 ":   -0.08
CHARGE, T4Y01, " C11":    0.09
CHARGE, T4Y01, " C12":    0.15
CHARGE, T4Y01, " C14":   -0.17
CHARGE, T4Y01, " C2 ":   -0.13
CHARGE, T4Y01, " C3 ":   -0.13
CHARGE, T4Y01, " C9 ":   -0.10
CHARGE, T4Y01, " H5 ":    0.13
CHARGE, T4Y01, " H6 ":    0.15
CHARGE, T4Y01, " H8 ":    0.04
CHARGE, T4Y01, " H7 ":    0.04
CHARGE, T4Y01, " H9 ":    0.04
CHARGE, T4Y01, " H10":    0.04
CHARGE, T4Y01, " H13":    0.06
CHARGE, T4Y01, " H14":    0.06
CHARGE, T4Y01, " H1 ":    0.04
CHARGE, T4Y01, " H  ":    0.04
CHARGE, T4Y01, " H2 ":    0.04
CHARGE, T4Y01, " H15":    0.05
CHARGE, T4Y01, " H16":    0.05
CHARGE, T4Y01, " H18":    0.03
CHARGE, T4Y01, " H17":    0.03
CHARGE, T4Y01, " H22":    0.06
CHARGE, T4Y01, " H19":    0.06
CHARGE, T4Y01, " H20":    0.06
CHARGE, T4Y01, " H3 ":    0.13
CHARGE, T4Y01, " H4 ":    0.13
CHARGE, T4Y01, " H11":    0.06
CHARGE, T4Y01, " H12":    0.06

tpl-free2mcce.py¶

This command converts ftpl files to ./param, a directory hosts old mcce tple files. It is a compatibility tool, which makes new ftpl files readable by old mcce executable.

Syntax

tpl-free2mcce.py

Input file:

run.prm
param/ under mcce distribution directory

Output file

param under current directory

tpl-mcce2free.py¶

Future versions of MCCE will use ftpl format, and this command converts mcce tpl file to new ftpl file.

Syntax

tpl-mcce2ftpl.py tplfile

Input file:

tpl file

Output file

ftpl file content on screen.

verify_ftpl.py¶

This program verifies a ftpl by reading a pdb file of that cofactor.

Syntax

verify_ftpl.py tplfile pdbfile

Input file:

ftpl file
pdb file that corresponds to that ftpl file

Connecting to other programs¶

striph2o.py¶

This tool strips away specified surface molecules layer by layer until all left are buried

Syntax

usage: striph2o.py [-h] [-c RES [RES ...]] [-s exposure] -f inputfile
                   [-o outputfile]

Strip off exposed cofactors like water and ions based on solvent accessible
surface area.

optional arguments:
  -h, --help        show this help message and exit
  -c RES [RES ...]  Specify cofactor names to strip off, default is HOH.
  -s exposure       Fraction exposure threshold to be cut. Default is 0.05.
  -f inputfile      Input file name.
  -o outputfile     Output file name, default is inputfile name with extension
                    .stripped.

This program does not only strip off water, it also strip off any molecule as named in the command line. So one can use it to delete ions and lipid bilayers in the input structure.

Required files:

input pdb file

Output files

input_file-stripped.pdb for stripped pdb file unless otherwise named
input_file.acc for residue solvent accessibility

Example:

striph2o.py -f frame32_50.pdb -c HOH CLA SOD BGA POP DLP

Last update: 2020-12-30