2018 AMBER tutorial with 2nnq

2nnq with an explicit solvent model

Prepare the files

Convert 2nnq.lig.withH.charged.mol2 to pdb in chimera

Convert 2nnq.rec.withH.charged.mol2 to pdb in chimera

Copy into zzz.master

Parameters

Move into 000.programs

Paramaterize the ligand

antechamber -i ../zzz.master/2nnq.lig.withH.charged.pdb -fi pdb -o 2nnq_lig.am1bcc.mol2 -fo mol2 -at gaff2 -c bcc -rn LIG -nc 1

Check for missing force field parameters

parmchk2 -i 2nnq_lig.am1bcc.mol2 -f mol2 -o 2nnq_lig.am1bcc.frcmod

TLeap

Move into 001.tleap_build

Create tleap.build.in file

#!/usr/bin/sh

###Load Protein force field                                                     
source leaprc.protein.ff14SB
###Load GAFF force field (for our ligand)                                       
source leaprc.gaff
###Load TIP3P (water) force field                                               
source leaprc.water.tip3p
####Load Ions frcmod for the tip3p model                                        
loadamberparams frcmod.ionsjc_tip3p
###Needed so we can use igb=8 model                                             
set default PBradii mbondi3

###Load Protein pdb file                                                        
rec=loadpdb ../zzz.master/2nnq.rec.withH.charged.pdb

###Load Ligand frcmod/mol2                                                      
loadamberparams ../000.parameters_2nnq/2nnq_lig.am1bcc.frcmod
lig=loadmol2 ../000.parameters_2nnq/2nnq_lig.am1bcc.mol2

###Create gas-phase complex                                                     
gascomplex= combine {rec lig}

###Write gas-phase pdb                                                          
savepdb gascomplex 2nnq.gas.complex.pdb

###Write gas-phase toplogy and coord files for MMGBSA calc                      
saveamberparm gascomplex 2nnq.gas.complex.prmtop 2nnq.gas.complex.rst7
saveamberparm rec 2nnq.gas.receptor.prmtop 2nnq.gas.receptor.rst7
saveamberparm lig 2nnq.gas.ligand.prmtop 2nnq.gas.ligand.rst7

###Create solvated complex (albeit redundant)                                   
solvcomplex= combine {rec lig}

###Solvate the system                                                           
solvateoct solvcomplex TIP3PBOX 12.0

###Neutralize system (it will add either Na or Cl depending on net charge)      
addions solvcomplex Cl- 0
addions solvcomplex Na+ 0

###Write solvated pdb file

###Create solvated complex (albeit redundant)                                   
solvcomplex= combine {rec lig}

###Solvate the system                                                           
solvateoct solvcomplex TIP3PBOX 12.0

###Neutralize system (it will add either Na or Cl depending on net charge)      
addions solvcomplex Cl- 0
addions solvcomplex Na+ 0

###Write solvated pdb file            

Create Amber topology and coordinates files for the MD simulation

tleap -f tleap.build.in