For internal use
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amber:setup
Table of Contents
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？
amber/setup.txt · Last modified: 2017/07/04 14:46 by 127.0.0.1
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