pdbNAMDRestraintCreate

pdbNAMDRestraintCreate is Eos's Command that creates the data for NAMD from PDB file.

List of option

Main option

Option	Essential/Optional	Description	Default
-i	Essential	Input: PDB	NULL
-r	Essential	Reference: PDB	NULL
-o	Optional	Output: NAMD Restraint	stdout
-O	Optional	Output: PDB Force	stdout
-kf	Optional	Input: Kf kcal/mol/A^2	1.0
-autokf	Optional	Input: Kf kcal/mol for averaged length	1.0
-seg	Optional	Input: segment name	EXAMPLE
-c	Optional	ConfigurationFile	NULL
-m	Optional	Mode	0
-h	Optional	Help

-autokf is prior to -kf.

-m details

Value	Description
0

Execution example

Input file image

Gravity Centre(CA) Atom far from Centre(CA) Atom far from Centre(CA, Axis)

6.053012e+00 9.408175e+00 2.622422e+01 3.286665e+01 24.77 22.88 23.78

Reference 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

-o 's data

urestraint {
    posi (EXAMPLE,1,ca) kf=1 ref=(-5.913,31.928,-6.676)
    posi (EXAMPLE,2,ca) kf=1 ref=(-4.759,28.93,-4.751)
    posi (EXAMPLE,3,ca) kf=1 ref=(-4.531,29.674,-1.062)
    posi (EXAMPLE,4,ca) kf=1 ref=(-2.465,27.513,1.336)
    posi (EXAMPLE,5,ca) kf=1 ref=(-3.586,27.58,4.978)

...

    posi (EXAMPLE,162,ca) kf=1 ref=(3.951,18.742,0.732)
    posi (EXAMPLE,163,ca) kf=1 ref=(0.404,20.135,0.49)
    posi (EXAMPLE,164,ca) kf=1 ref=(0.711,20.05,-3.346)
    posi (EXAMPLE,165,ca) kf=1 ref=(1.52,16.308,-3.145)
    posi (EXAMPLE,166,ca) kf=1 ref=(-1.217,15.28,-0.638)
}

-O 's data

Gravity Centre(CA) Atom far from Centre(CA) Atom far from Centre(CA, Axis)

0.000000e+00 1.578772e+01 -1.433346e+01 2.132370e+01 0.00 15.79 14.33

Option -kf

Case: kf=2

-o 's data

urestraint {
    posi (EXAMPLE,1,ca) kf=2 ref=(-5.913,31.928,-6.676)
    posi (EXAMPLE,2,ca) kf=2 ref=(-4.759,28.93,-4.751)
    posi (EXAMPLE,3,ca) kf=2 ref=(-4.531,29.674,-1.062)
    posi (EXAMPLE,4,ca) kf=2 ref=(-2.465,27.513,1.336)
    posi (EXAMPLE,5,ca) kf=2 ref=(-3.586,27.58,4.978)

...

    posi (EXAMPLE,162,ca) kf=2 ref=(3.951,18.742,0.732)
    posi (EXAMPLE,163,ca) kf=2 ref=(0.404,20.135,0.49)
    posi (EXAMPLE,164,ca) kf=2 ref=(0.711,20.05,-3.346)
    posi (EXAMPLE,165,ca) kf=2 ref=(1.52,16.308,-3.145)
    posi (EXAMPLE,166,ca) kf=2 ref=(-1.217,15.28,-0.638)
}

-O 's data

Gravity Centre(CA) Atom far from Centre(CA) Atom far from Centre(CA, Axis)

0.000000e+00 3.157545e+01 -2.866693e+01 4.264741e+01 0.00 31.58 28.67

Option -autokf

Case: autokf=2

-o 's data

urestraint {
    posi (EXAMPLE,1,ca) kf=0.186306 ref=(-5.913,31.928,-6.676)
    posi (EXAMPLE,2,ca) kf=0.186306 ref=(-4.759,28.93,-4.751)
    posi (EXAMPLE,3,ca) kf=0.186306 ref=(-4.531,29.674,-1.062)
    posi (EXAMPLE,4,ca) kf=0.186306 ref=(-2.465,27.513,1.336)
    posi (EXAMPLE,5,ca) kf=0.186306 ref=(-3.586,27.58,4.978)

...

    posi (EXAMPLE,162,ca) kf=0.186306 ref=(3.951,18.742,0.732)
    posi (EXAMPLE,163,ca) kf=0.186306 ref=(0.404,20.135,0.49)
    posi (EXAMPLE,164,ca) kf=0.186306 ref=(0.711,20.05,-3.346)
    posi (EXAMPLE,165,ca) kf=0.186306 ref=(1.52,16.308,-3.145)
    posi (EXAMPLE,166,ca) kf=0.186306 ref=(-1.217,15.28,-0.638)
}

-O 's data

Gravity Centre(CA) Atom far from Centre(CA) Atom far from Centre(CA, Axis)

0.000000e+00 2.941331e+00 -2.670398e+00 3.972714e+00 0.00 2.94 2.67

Option -seg

Case: seg=SEGNAME

-o 's data

urestraint {
    posi (SEGNAME,1,ca) kf=1 ref=(-5.913,31.928,-6.676)
    posi (SEGNAME,2,ca) kf=1 ref=(-4.759,28.93,-4.751)
    posi (SEGNAME,3,ca) kf=1 ref=(-4.531,29.674,-1.062)
    posi (SEGNAME,4,ca) kf=1 ref=(-2.465,27.513,1.336)
    posi (SEGNAME,5,ca) kf=1 ref=(-3.586,27.58,4.978)

...

    posi (SEGNAME,162,ca) kf=1 ref=(3.951,18.742,0.732)
    posi (SEGNAME,163,ca) kf=1 ref=(0.404,20.135,0.49)
    posi (SEGNAME,164,ca) kf=1 ref=(0.711,20.05,-3.346)
    posi (SEGNAME,165,ca) kf=1 ref=(1.52,16.308,-3.145)
    posi (SEGNAME,166,ca) kf=1 ref=(-1.217,15.28,-0.638)
}