ParmEd

Introduction

This is going to illustrate how we change a parameter files in amber？
refchapter 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:

* 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).

Example:

change CHARGE :ASP@N -0.5163
#where CHARGE is given in units of elementary atomic charges!!!

2.setAngle

Use this to change or add a non-exist angle in topology files
Usage:setAngle <mask1> <mask2> <mask3> <k> <THETeq>

Example:

setAngle @%O2 @%Zn @%NB 50 105.00
#where ktheta is in kcal/mol/(rad^2),THETeq is in rad

3.setBond

Use this to change or add a non-exist bond in topology files
Usage:setBond <mask1> <mask2> <k> <Req>

Example:

setBond @%O2 @%Zn 120 1.92
#where kr is in kcal/mol/(Angstrom^2),Req is in Angstrom

Propka

Introduction

This is going to illustrate how we protonate a pdb structure？
ref

Table of Contents

ParmEd

Introduction

COMMAND

1.change

2.setAngle

3.setBond

Propka

Introduction