2019 AMBER tutorial with PDBID 2BXF

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2BXF with an explicit solvent model

Prepare the files

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

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

Copy into zzz.master

Parameters

The system we are working on has two main components (Protein receptor & ligand). The usual forcefield "ff14SB" contains all the parameters needed for calculations of the protein. However, the ligand is a non-protein component. Therefore, ff14SB forcefield does not contain the parameters needed for the calculations regarding the ligand. Therefore, we need to generate parameters needed for the ligand. The following steps will be taken using antechamber in order to generate the ligand parameters.

Move into 000.programs

Paramaterize the ligand 

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

Check for missing force field parameters 

parmchk2 -i 2BXF_lig.am1bcc.mol2 -f mol2 -o 2BXF_lig.am1bcc.frcmod
  1. !/usr/bin/sh
      1. Load Protein force field

source leaprc.protein.ff14SB

      1. Load GAFF force field (for our ligand)

source leaprc.gaff

      1. Load TIP3P (water) force field

source leaprc.water.tip3p

        1. Load Ions frcmod for the tip3p model

loadamberparams frcmod.ionsjc_tip3p

      1. Needed so we can use igb=8 model

set default PBradii mbondi3


      1. Load Protein pdb file

rec=loadpdb ../zzz.master/backup.pdb bond rec.49.SG rec.58.SG bond rec.241.SG rec.249.SG bond rec.71.SG rec.87.SG bond rec.86.SG rec.97.SG bond rec.120.SG rec.165.SG bond rec.164.SG rec.173.SG bond rec.510.SG rec.555.SG bond rec.472.SG rec.482.SG bond rec.457.SG rec.473.SG bond rec.196.SG rec.242.SG bond rec.261.SG rec.275.SG bond rec.312.SG rec.357.SG bond rec.274.SG rec.285.SG bond rec.388.SG rec.434.SG bond rec.433.SG rec.444.SG bond rec.554.SG rec.563.SG bond rec.356.SG rec.365.SG

      1. Load Ligand frcmod/mol2

loadamberparams ../000.parameters/2BXF_lig.am1bcc.frcmod lig=loadmol2 ../000.parameters/2BXF_lig.am1bcc.mol2

      1. Create gas-phase complex

gascomplex= combine {rec lig}

      1. Write gas-phase pdb

savepdb gascomplex 2BXF.gas.complex.pdb

      1. Write gas-phase toplogy and coord files for MMGBSA calc

saveamberparm gascomplex 2BXF.gas.complex.prmtop 2BXF.gas.complex.rst7 saveamberparm rec 2BXF.gas.receptor.prmtop 2BXF.gas.receptor.rst7 saveamberparm lig 2BXF.gas.ligand.prmtop 2BXF.gas.ligand.rst7

      1. Create solvated complex (albeit redundant)

solvcomplex= combine {rec lig}

      1. Solvate the system

solvateoct solvcomplex TIP3PBOX 12.0

      1. Neutralize system (it will add either Na or Cl depending on net charge)

addions solvcomplex Cl- 0 addions solvcomplex Na+ 0

      1. Write solvated pdb file

savepdb solvcomplex 2BXF.wet.complex.pdb

      1. Check the system

charge solvcomplex check solvcomplex

      1. Write Solvated topology and coord file

saveamberparm solvcomplex 2BXF.wet.complex.prmtop 2BXF.wet.complex.rst7 

#!/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/backup.pdb
bond rec.49.SG  rec.58.SG
bond rec.241.SG rec.249.SG
bond rec.71.SG  rec.87.SG
bond rec.86.SG  rec.97.SG
bond rec.120.SG rec.165.SG
bond rec.164.SG rec.173.SG
bond rec.510.SG rec.555.SG
bond rec.472.SG rec.482.SG
bond rec.457.SG rec.473.SG
bond rec.196.SG rec.242.SG
bond rec.261.SG rec.275.SG
bond rec.312.SG rec.357.SG
bond rec.274.SG rec.285.SG
bond rec.388.SG rec.434.SG
bond rec.433.SG rec.444.SG
bond rec.554.SG rec.563.SG
bond rec.356.SG rec.365.SG

###Load Ligand frcmod/mol2
loadamberparams ../000.parameters/2BXF_lig.am1bcc.frcmod
lig=loadmol2 ../000.parameters/2BXF_lig.am1bcc.mol2

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

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

###Write gas-phase toplogy and coord files for MMGBSA calc
saveamberparm gascomplex 2BXF.gas.complex.prmtop 2BXF.gas.complex.rst7
saveamberparm rec 2BXF.gas.receptor.prmtop 2BXF.gas.receptor.rst7
saveamberparm lig 2BXF.gas.ligand.prmtop 2BXF.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
savepdb solvcomplex 2BXF.wet.complex.pdb

###Check the system
charge solvcomplex
check solvcomplex

###Write Solvated topology and coord file
saveamberparm solvcomplex 2BXF.wet.complex.prmtop 2BXF.wet.complex.rst7

#!/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/backup.pdb
bond rec.49.SG  rec.58.SG
bond rec.241.SG rec.249.SG
bond rec.71.SG  rec.87.SG
bond rec.86.SG  rec.97.SG
bond rec.120.SG rec.165.SG
bond rec.164.SG rec.173.SG
bond rec.510.SG rec.555.SG
bond rec.472.SG rec.482.SG
bond rec.457.SG rec.473.SG
bond rec.196.SG rec.242.SG
bond rec.261.SG rec.275.SG
bond rec.312.SG rec.357.SG
bond rec.274.SG rec.285.SG
bond rec.388.SG rec.434.SG
bond rec.433.SG rec.444.SG
bond rec.554.SG rec.563.SG
bond rec.356.SG rec.365.SG

###Load Ligand frcmod/mol2
loadamberparams ../000.parameters/2BXF_lig.am1bcc.frcmod
lig=loadmol2 ../000.parameters/2BXF_lig.am1bcc.mol2

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

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

###Write gas-phase toplogy and coord files for MMGBSA calc
saveamberparm gascomplex 2BXF.gas.complex.prmtop 2BXF.gas.complex.rst7
saveamberparm rec 2BXF.gas.receptor.prmtop 2BXF.gas.receptor.rst7
saveamberparm lig 2BXF.gas.ligand.prmtop 2BXF.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
savepdb solvcomplex 2BXF.wet.complex.pdb

###Check the system
charge solvcomplex
check solvcomplex

###Write Solvated topology and coord file
saveamberparm solvcomplex 2BXF.wet.complex.prmtop 2BXF.wet.complex.rst7

#!/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/backup.pdb
bond rec.49.SG  rec.58.SG
bond rec.241.SG rec.249.SG
bond rec.71.SG  rec.87.SG
bond rec.86.SG  rec.97.SG
bond rec.120.SG rec.165.SG
bond rec.164.SG rec.173.SG
bond rec.510.SG rec.555.SG
bond rec.472.SG rec.482.SG
bond rec.457.SG rec.473.SG
bond rec.196.SG rec.242.SG
bond rec.261.SG rec.275.SG
bond rec.312.SG rec.357.SG
bond rec.274.SG rec.285.SG
bond rec.388.SG rec.434.SG
bond rec.433.SG rec.444.SG
bond rec.554.SG rec.563.SG
bond rec.356.SG rec.365.SG
###Load Ligand frcmod/mol2
loadamberparams ../000.parameters/2BXF_lig.am1bcc.frcmod
lig=loadmol2 ../000.parameters/2BXF_lig.am1bcc.mol2
###Create gas-phase complex
gascomplex= combine {rec lig}
###Write gas-phase pdb
savepdb gascomplex 2BXF.gas.complex.pdb
###Write gas-phase toplogy and coord files for MMGBSA calc
saveamberparm gascomplex 2BXF.gas.complex.prmtop 2BXF.gas.complex.rst7
saveamberparm rec 2BXF.gas.receptor.prmtop 2BXF.gas.receptor.rst7
saveamberparm lig 2BXF.gas.ligand.prmtop 2BXF.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
savepdb solvcomplex 2BXF.wet.complex.pdb
###Check the system
charge solvcomplex
check solvcomplex
###Write Solvated topology and coord file
saveamberparm solvcomplex 2BXF.wet.complex.prmtop 2BXF.wet.complex.rst7
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