119
Conformational analysis: Analysis of the resulting trajectories is
performed with the cpptraj module [30] of AMBER. The cpptraj
functionality is able to calculate a variety of properties, such as distances, angles, torsions, RMSD, hydrogen bonds, fluctuations,
J-coupling, surface areas, radii of gyration, average structures, diffusion, and radial distribution functions, among many others.
Here, we provide a representative example of an input (ptraj.in),
which includes distance, RMSD, and fluctuation calculations
(see Note 8).
Execute in AMBER: cpptraj complexparm.top ptraj.in
Output files are not included in the above command line as
they are generated from cpptraj after they have been included in
the ptraj.in file.
4 Notes
1. A simplified Gaussian input file for the geometry optimization
and ESP generation of IRB (IRB.com) is shown below:
IRB.com
--Link1- %chk=molecule
#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2)
iop(6/42=6) opt nosymm
remark line goes here
0 1
##Author’s note: The initial X- Y- Z coordinates
of IRB follow here (not shown).
2. The RESP charges for 2-HP-β-CD are manually assigned to
each atom in tLEaP. The following command is an example for
charge assignment to the oxygen atom, which is labeled “O2”
and belongs to the first residue (HP group) of 2-HP-β-CD:
set a.1.O2 charge −0.631696
Similar command lines should be included in tLEaP for each
2-HP-β-CD atom and its respective RESP charge.
3. Input files for complex minimization with AMBER. Next to
each command, a short explanation is offered in italics:
Min1.in
Minimization of system keeping complex fixed
&cntrl
imin=1, Perform minimization
maxcyc=10000, The total number of cycles per
formed
ncyc=5000, First 5000 cycles with steepest descent before switching to conjugate gradient
cut=10.0, Cutoff for nonbonded interactions
ntb=1, Constant volume
3.5 Conformational
Analysis
Molecular Dynamics and Drug Complexation with Cyclodextrins
Conformational analysis: Analysis of the resulting trajectories is
performed with the cpptraj module [30] of AMBER. The cpptraj
functionality is able to calculate a variety of properties, such as distances, angles, torsions, RMSD, hydrogen bonds, fluctuations,
J-coupling, surface areas, radii of gyration, average structures, diffusion, and radial distribution functions, among many others.
Here, we provide a representative example of an input (ptraj.in),
which includes distance, RMSD, and fluctuation calculations
(see Note 8).
Execute in AMBER: cpptraj complexparm.top ptraj.in
Output files are not included in the above command line as
they are generated from cpptraj after they have been included in
the ptraj.in file.
4 Notes
1. A simplified Gaussian input file for the geometry optimization
and ESP generation of IRB (IRB.com) is shown below:
IRB.com
--Link1- %chk=molecule
#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2)
iop(6/42=6) opt nosymm
remark line goes here
0 1
##Author’s note: The initial X- Y- Z coordinates
of IRB follow here (not shown).
2. The RESP charges for 2-HP-β-CD are manually assigned to
each atom in tLEaP. The following command is an example for
charge assignment to the oxygen atom, which is labeled “O2”
and belongs to the first residue (HP group) of 2-HP-β-CD:
set a.1.O2 charge −0.631696
Similar command lines should be included in tLEaP for each
2-HP-β-CD atom and its respective RESP charge.
3. Input files for complex minimization with AMBER. Next to
each command, a short explanation is offered in italics:
Min1.in
Minimization of system keeping complex fixed
&cntrl
imin=1, Perform minimization
maxcyc=10000, The total number of cycles per
formed
ncyc=5000, First 5000 cycles with steepest descent before switching to conjugate gradient
cut=10.0, Cutoff for nonbonded interactions
ntb=1, Constant volume
3.5 Conformational
Analysis
Molecular Dynamics and Drug Complexation with Cyclodextrins