======ParmEd======
=====Introduction======
    * This is going to illustrate how we change a parameter files in amber？
    * [[http://ambermd.org/doc12/Amber17.pdf|ref]]chapter 14
    * Please change your parameter files using this instead of edit manually!!! 
=====COMMAND=====
====1.change====
    * Use this if you want to change charge of atoms recalculated by Gaussian for specific case.
    * Usage:change <property> <atom_mask> <new_value>
            * properties list:<code>
* CHARGE (given in units of elementary atomic charges)
* MASS (in g/mol)
* RADII (in Angstroms, these are the GB radii)
* SCREEN (the GB screening parameters)
* ATOM_NAME
* AMBER_ATOM_TYPE (this is NOT the van der Waals type). </code>
    * Example:<code>change CHARGE :ASP@N -0.5163
#where CHARGE is given in units of elementary atomic charges!!!</code>

====2.setAngle====
    * Use this to change or add a non-exist angle in topology files
    * Usage:setAngle <mask1> <mask2> <mask3> <k> <THETeq>
    * Example:<code>setAngle @%O2 @%Zn @%NB 50 105.00
#where ktheta is in kcal/mol/(rad^2),THETeq is in rad</code>

====3.setBond====
    * Use this to change or add a non-exist bond in topology files
    * Usage:setBond <mask1> <mask2> <k> <Req>
    * Example:<code>setBond @%O2 @%Zn 120 1.92
#where kr is in kcal/mol/(Angstrom^2),Req is in Angstrom</code>

======Propka======
=====Introduction======
    * This is going to illustrate how we protonate a pdb structure？
    * [[https://github.com/jensengroup/propka-3.1|ref]]