pdbWaterAdd

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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