pdbWaterAdd

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pdbWaterAdd is Eos's Command that adds water molecules around the input file. Output file is structured at water molecules only.


List of option

Main option

Option Essential/Optional Description Default
-i Essential Input: PDB NULL
-o Essential Output: PDB NULL
-d Optional Density of Water: [M] 55.55555
-r Optional Radius of Water Volume(for m=0, 1) 100
-height Optional Height of Water Volume(for m=1) 100
-cube Optional (X, Y, Z): [A](for m=3) (100, 100, 100)
-edge Optional layer number(for m=2) 3
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-h Optional Help  

-m details

Value Description
0 sphere
1 cylinder
2 Edge
3 Cube


Execution example

Input file image

Input-121P-PDB.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

6.053012e+00 2.519590e+01 1.189075e+01

3.286664e+01

24.77 23.85 28.04


Case: Options only essential

White is Input file.
Outdata-pdbWaterAdd.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

9.330483e+00 2.794594e+01 1.553714e+01

1.010862e+02

100.31 100.22 100.46


Option -r

Case: r=30

White is Input file.
Outdata-r-pdbWaterAdd.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.013427e+01 2.852403e+01 1.641233e+01

3.179522e+01

29.60 29.31 29.34


Option -d

Case: d=100, r=30

White is Input file.
Outdata-d-pdbWaterAdd.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.088372e+01 2.846397e+01 1.583489e+01

3.126308e+01

29.54 29.43 29.34


Option -m

Case: m=1

Case: No other settings
White is Input file.
Outdata-m1-pdbWaterAdd.png


Outdata-m1(yz)-pdbWaterAdd.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

9.336175e+00 2.794978e+01 1.554270e+01

1.124455e+02

100.48 100.40 51.18


Case: height=50, r=30
White is Input file.
Outdata-m1height-pdbWaterAdd.png Outdata-m1height(yz)-pdbWaterAdd.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

9.900170e+00 2.835893e+01 1.610196e+01

3.983113e+01

29.49 29.53 26.50


Case: m=2

Case: No other settings
White is Input file.
Outdata-m2-pdbWaterAdd.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

2.902557e+00 2.626757e+01 1.201421e+01

4.315685e+01

32.09 31.73 33.16


Case: edge=1
White is Input file.
Outdata-m2edge-pdbWaterAdd.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

3.767874e+00 2.603396e+01 1.347542e+01

3.475105e+01

25.49 26.98 29.59


Case: m=3

Case: No other settings
White is Input file.
Outdata-m3-pdbWaterAdd.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

7.796508e+00 2.639248e+01 1.400760e+01

8.374090e+01

49.54 49.47 49.50


Case: cube=(150, 50, 25)
White is Input file.
Outdata-m3cube-pdbWaterAdd.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

8.101933e+00 2.262963e+01 1.431665e+01

4.112811e+01

24.75 25.55 24.59