Child pages
  • DNA force field including e/z OL1 - chi OL4

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

This is an example of the tleap file:

 

...

----------------------------------------------
source leaprc.ff14SB

addPath Param-99bsc0-ez1-ol4-for-DNA

...

loadoff dna-chiOL4-ezOL1.lib
ez = loadamberparams frcmod-ez1-bsc0.dat
chi = loadamberparams frcmod.OL4.chi
dna = loadpdb dna.pdb

 

----------------------------------------------

This tleap file will load the most recent force field for proteins/DNA/RNA which is called ff14SB.  
Then, it will set as a path the location of the files with the modifications are. In this case, it is just the name of the directory where we downloaded the file.  Make sure you set the full path.
The addatomtypes is very important because the modifications requires new atom types so add the section exactly.
The loadoff command loads the library of the nucleotides with the new atom types and then the comand loadamberparams loads the individual modifications, one for the epsilon/zeta dihedral angle and another for a revised version of the chi torsion.  In In the above example, a PDB file called dna.pdb is loaded to check that the parameters are loaded and everything works correctly.

After this, it is ready, you can just load a PDB with a double stranded DNA and when you generate the AMBER topology and coordinate file, it will be including the e/z OL1 and chi OL4 modifications.

 

The tleap file can be run using: 

tleap -s -f <file name>


Content by Label
showLabelsfalse
max5
spacesamber
sortmodified
showSpacefalse
reversetrue
typepage
labelskb-how-to-article

...