51
In your Linux terminal, use the relevant commands to load the
Gromacs software (e.g., ./gromacsxxxx.x or module load gromacs/xxxx.x if you are running on an HPC server).
1. For the study of CC:2-HP-B-CD complex, after loading gromacs, go to your working directory (where all the files that you
have created reside) and use the following terminal
commands:
gmx_d editconf –f CC.pdb –o CC.gro
gmx_d editconf –f 2-HP-B-CD.pdb –o 2-HP-B-CD.
gro
The command gmx_d calls the gromacs software to operate
in double precision while the module editconf converts the .pdb
format to the appropriate gromacs input format .gro. Now two
separate input files have been created.
2. In order to create an input file for the CC:2-HP-B-CD complex, copy the 2-HP-B-CD.gro to a new file and name it complex.gro using the following terminal commands:
cp 2-HP-B-CD.gro complex.gro
3. Open CC.gro in a text editor by pressing:
vi CC.gro
The first two lines are the title and the number of atoms;
keep the number of atoms in mind. In the third line and first
column you will see the name that has been given to your molecule. In case the molecule reads 1LIG (or exactly the same as
the 2-HP-B-CD molecule) change its molecule name. To do
so, if you are using vi press the following:
:%s/LIG/CC and press Enter
in order to name the molecule CC (or use any name you
like).
Ignore the first two lines and copy the rest, which are the
molecule’s coordinates.
In order to avoid any future errors, make sure that the same
name for the molecule is used in the .gro file, the .itp file (in
sections [ moleculetype ] and [ atoms ]/resid ) and topol.top
(the topol.top will be described in the next step).
4. Open the complex.gro file and paste the coordinates that you
just copied, before the last line which is the cell’s vectors. Make
sure that everything is aligned properly on the right. After copying the coordinates of the drug molecule in the host’s input file,
correct the number of coordinates in the second line of the .gro
file, by adding up the number of coordinates copied. For example the number 217 for 2-HP-B-CD should be changed to 296
after having copied the coordinates for the 79 atoms of CC.
3.1.4 Create the
Gromacs Input Files
Study of Candesartan Cilexetil: 2-Hydroxypropyl-β-Cyclodextrin Interactions…
In your Linux terminal, use the relevant commands to load the
Gromacs software (e.g., ./gromacsxxxx.x or module load gromacs/xxxx.x if you are running on an HPC server).
1. For the study of CC:2-HP-B-CD complex, after loading gromacs, go to your working directory (where all the files that you
have created reside) and use the following terminal
commands:
gmx_d editconf –f CC.pdb –o CC.gro
gmx_d editconf –f 2-HP-B-CD.pdb –o 2-HP-B-CD.
gro
The command gmx_d calls the gromacs software to operate
in double precision while the module editconf converts the .pdb
format to the appropriate gromacs input format .gro. Now two
separate input files have been created.
2. In order to create an input file for the CC:2-HP-B-CD complex, copy the 2-HP-B-CD.gro to a new file and name it complex.gro using the following terminal commands:
cp 2-HP-B-CD.gro complex.gro
3. Open CC.gro in a text editor by pressing:
vi CC.gro
The first two lines are the title and the number of atoms;
keep the number of atoms in mind. In the third line and first
column you will see the name that has been given to your molecule. In case the molecule reads 1LIG (or exactly the same as
the 2-HP-B-CD molecule) change its molecule name. To do
so, if you are using vi press the following:
:%s/LIG/CC and press Enter
in order to name the molecule CC (or use any name you
like).
Ignore the first two lines and copy the rest, which are the
molecule’s coordinates.
In order to avoid any future errors, make sure that the same
name for the molecule is used in the .gro file, the .itp file (in
sections [ moleculetype ] and [ atoms ]/resid ) and topol.top
(the topol.top will be described in the next step).
4. Open the complex.gro file and paste the coordinates that you
just copied, before the last line which is the cell’s vectors. Make
sure that everything is aligned properly on the right. After copying the coordinates of the drug molecule in the host’s input file,
correct the number of coordinates in the second line of the .gro
file, by adding up the number of coordinates copied. For example the number 217 for 2-HP-B-CD should be changed to 296
after having copied the coordinates for the 79 atoms of CC.
3.1.4 Create the
Gromacs Input Files
Study of Candesartan Cilexetil: 2-Hydroxypropyl-β-Cyclodextrin Interactions…