Use AMBER forcefields in NAMD
- Online resources
The official website of AMBER forcefield contains lots of useful information. Relevant parameters in NAMD to enable AMBER forcefield are explained NAMD’s Userguide. Correspondence between the parameters in NAMD2.7 and those in Amber11 is explained in here.
Tutorials:
[1] Introduction to MD using AMBER
[2] Build Protein Systems in Explicit Solvent
Starting from a PDB file, we use LEaP from the package AmberTools22 to build necessary parameter files. AmberTools22 can be installed via conda, as described here.
- Examples
We show how to create the parameter files for Alanine dipeptide and chignolin in order to run MD simulations with AMBER forcefield. The configuration file needed to run MD in NAMD can be prepared following the discussions in [1] and [2] above. See this post on how to obtain the PDB files of these two systems.
2.1. Alanine dipeptide
The parameter file for Alanine dipeptide in vacuum can be built simply using the following commands in tleap:
source leaprc.protein.ff19SB
diala = sequence { ACE ALA NME }
saveamberparm diala ad.prmtop ad.inpcrd
or using a PDB file:
source leaprc.protein.ff19SB
ramp=loadpdb ad.pdb
saveamberparm ramp ad.prmtop ad.inpcrd
To build the parameter file that describes the system in water, use:
source leaprc.protein.ff14SB
diala = sequence { ACE ALA NME }
source leaprc.water.tip3p
solvateoct diala TIP3PBOX 10.0
saveamberparm diala ad.prmtop ad.inpcrd
2.2. Chignolin
In vacuum:
source leaprc.protein.ff19SB
ramp=loadpdb 5awl.pdb
saveamberparm ramp 5awl.prmtop 5awl.inpcrd
In water:
source leaprc.protein.ff19SB
source leaprc.water.tip3p
ramp=loadpdb 5awl.pdb
addIons ramp Na+ 0
solvateOct ramp TIP3PBOX 10.0
saveamberparm ramp 5awl.prmtop 5awl.inpcrd