VMD instructions for AMBERff-in-NAMD

Amber FF on VMD

Using AMBER forcefield in VMD 1.9.4

VMD 2.0 will ship with AMBER force field, but previous versions (VMD 1.9.x) require manual installation of forcefield files and updated scripts.

Step 1: Download the updated solvate and ionize plugins and force field files.

The Amber force field files topology and parameters files in CHARMM format were made available from Hadden Lab in the following link

git clone https://github.com/Hadden-lab/AMBERff-in-NAMD

Please cite their article when using this files
AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD
Santiago Antolínez, Peter Eugene Jones, James C. Phillips, and Jodi A. Hadden-Perilla
Journal of Chemical Information and Modeling 2024 64 (2), 543-554
DOI: 10.1021/acs.jcim.3c01648

Step 2: Add amber forcefield path to .vmdrc

Append following the path to your .vmdrc file. /home/username/.vmdrc

#Append path to AMBER cognizant plugins
lappend auto_path /path/to/AMBERff-in-NAMD/plugins

Step 3: Preparing an AMBER topology in VMD 1.9.4, using PSFGEN

VMD 2.0 implements AMBER as a force field option in QwikMD 2.0, for VMD 1.9.4 or if you want to run it manually, here is how to proceed:

# Use PSFGEN 
package require psfgen
resetpsf

# Set the appropriate path to where you downloaded AMBER FF
set topdir /path/to/AMBERff-in-NAMD

# Load topologies.
topology $topdir/ff14SB/ff14SB.rtf
topology $topdir/solvents/opc_ions.str 

# Load protein pdb with AMBER atom and residue names
set molid [mol new structure.pdb]

# Select protein only and define a segment.
set sel [atomselect $molid protein] $sel set segname PTN
$sel writepdb protein.pdb

# Clean up selection
$sel delete

# Create protein segment, generate topology
# psfgen will add missing atoms and hydrogens as described in their .rtf topologies
segment PTN {pdb protein.pdb}
coordpdb protein.pdb PTN
regenerate angles dihedrals
guesscoord

# Write the topology and coordinates
writepsf solute.psf
writepdb solute.pdb

# Clean up previous molecule
mol delete $molid 

# Load the new one
set molid [mol new solute.psf]
mol addfile solute.pdb

# Load the new solvate 1.8 plugin with AMBER support.
package require solvate 1.8

# Solvate with OPC water model using -ambersolvent flag
solvate solute.psf solute.pdb -t 10 -o solvated -ambersolvent opc 

# Load the new autoionize 1.6 plugin, with AMBER support. (-amber flag)
package require autoionize 1.6
autoionize -psf solvated.psf -pdb solvated.pdb -cation NA -anion CL -sc 0.150 -o ionized -seg ION -amber 

# You're ready to go!
Place text and figures here.