116
source leaprc.water.tip3p
(iv) Load missing parameters file for IRB and 2-HP
loadamberparams IRB.frcmod
loadamberparams 2-HP-β-CD.frcmod
(v) Load library files for IRB and 2-HP:
loadoff IRB.lib
loadoff 2-HP.lib
(vi) Load IRB:2-HP-β-CD complex file:
a = loadpdb complex.pdb
(vii) Assign pre-calculated RESP atomic charges to 2-HP-β-CD
(see Note 2).
(viii) Add a truncated octahedral box containing TIP3P water
molecules around the complex. The edge of the periodic box
is set to be at least 16 Å away from each complex atom:
solvateoct a TIP3PBOX 16
(ix) Save topology (complexparm.top), coordinates (complexparm.crd), and PDB (complex_final.pdb) files of the
complex:
saveamberparm a complexparm.top complex
parm.crd
savepdb a complex_final.pdb
The detailed preparatory steps for MD and the actual production
MD run are described below. The MD calculations are performed
with the GPU version of PMEMD [22] from AMBER 16.
Complexes are minimized in three stages for 10,000 cycles each.
Minimization is performed with the steepest descent method for
the first 5000 steps and the conjugate gradient algorithm follows
for the next 5000 steps. The first step considers the complex practically fixed with the application of a harmonic force constant of
500 kcal mol
−1
Å
−2
, thus allowing the structures of the water molecules to relax. During the second step, the restraint was reduced
to 10 kcal mol
−1
Å
−2
, and finally all atoms were totally unrestrained
to move. A nonbonded cutoff of 10.0 Å is applied under constant
volume. The three input files are provided and explained in Note
3. An example of the command to perform minimization is
srun /amber16/bin/pmemd -O -i Min1.in -o complex_min1.out -p complexparm.top -c complexparm.crd -r complex_min1.rst
Note the use of complexparm.top/crd files, which were generated from Subheading. 3.2; the complex_min1.rst file will be used
as the input for the second stage of minimization and so on. Output
file complex_min1.out contains the energy information for every
step of the run.
3.3 Molecular
Dynamics Simulation
of the Complex
3.3.1 Energy
Minimization
Georgios Leonis et al.
source leaprc.water.tip3p
(iv) Load missing parameters file for IRB and 2-HP
loadamberparams IRB.frcmod
loadamberparams 2-HP-β-CD.frcmod
(v) Load library files for IRB and 2-HP:
loadoff IRB.lib
loadoff 2-HP.lib
(vi) Load IRB:2-HP-β-CD complex file:
a = loadpdb complex.pdb
(vii) Assign pre-calculated RESP atomic charges to 2-HP-β-CD
(see Note 2).
(viii) Add a truncated octahedral box containing TIP3P water
molecules around the complex. The edge of the periodic box
is set to be at least 16 Å away from each complex atom:
solvateoct a TIP3PBOX 16
(ix) Save topology (complexparm.top), coordinates (complexparm.crd), and PDB (complex_final.pdb) files of the
complex:
saveamberparm a complexparm.top complex
parm.crd
savepdb a complex_final.pdb
The detailed preparatory steps for MD and the actual production
MD run are described below. The MD calculations are performed
with the GPU version of PMEMD [22] from AMBER 16.
Complexes are minimized in three stages for 10,000 cycles each.
Minimization is performed with the steepest descent method for
the first 5000 steps and the conjugate gradient algorithm follows
for the next 5000 steps. The first step considers the complex practically fixed with the application of a harmonic force constant of
500 kcal mol
−1
Å
−2
, thus allowing the structures of the water molecules to relax. During the second step, the restraint was reduced
to 10 kcal mol
−1
Å
−2
, and finally all atoms were totally unrestrained
to move. A nonbonded cutoff of 10.0 Å is applied under constant
volume. The three input files are provided and explained in Note
3. An example of the command to perform minimization is
srun /amber16/bin/pmemd -O -i Min1.in -o complex_min1.out -p complexparm.top -c complexparm.crd -r complex_min1.rst
Note the use of complexparm.top/crd files, which were generated from Subheading. 3.2; the complex_min1.rst file will be used
as the input for the second stage of minimization and so on. Output
file complex_min1.out contains the energy information for every
step of the run.
3.3 Molecular
Dynamics Simulation
of the Complex
3.3.1 Energy
Minimization
Georgios Leonis et al.