Tutorial 3: A Protein and its Covalently Bonded Ligand

In this tutorial, we will show you how to use pdbtop to prepare a protein and its covalently bonded ligand for calculations.

Before we start, please make sure you have read Tutorial 1: A Standard Protein and Tutorial 2: Ligand Preparation.

Combine Protein and Ligand

Now we combine the protein and ligand. For coordinates, we just paste the content of 92v-1.pdb (see Tutorial 2: Ligand Preparation) at the end of 5vbm-4.pdb (see Tutorial 1: A Standard Protein) (before END statement), and save it to a new file, say 5vbm-92v.pdb.

For topology, we can mergy (-m) their PSF files:

$ pdbtop psf -m "5vbm-4.psf 92v-2.psf" -o 5vbm-92v

Note that the order of PSF files must MATCH* the order of PDB files.

Now we look at the strucure:

So, we must treat the covalent bond between the protein and ligand.

To build a bond between SG of CYS72 (the 1081-th atom) and S24 (the 2686-th atom) of 92V. We have to modify the topology. Now we add a bond:

$ pdbtop modify -i 5vbm-92v.pdb -t 5vbm-92v.psf --add-bonds "1081 2686" -o 5vbm-92v-1

Before proceeding, we note that HG1 at CYS72 (the 1082-th atom) is to be deleted, so we adjust the charge to keep the total charge of the system constant. In 5vbm-92v-1.psf, we note that:

5vbm-92v-1.psf

...
1080 A       72    CYS  HB2  HA        0.090000        1.0080           0
1081 A       72    CYS  SG   S        -0.230000       32.0600           0
1082 A       72    CYS  HG1  HS        0.160000        1.0080           0
1083 A       73    ARG  N    NH1      -0.470000       14.0070           0
1084 A       73    ARG  HN   H         0.310000        1.0080           0
...

So we add the charge of HG1 to SG, and set the charge of HG1 to zero, and save it to a new file, say 5vbm-92v-2.psf:

5vbm-92v-2.psf

...
1080 A       72    CYS  HB2  HA        0.090000        1.0080           0
1081 A       72    CYS  SG   S        -0.070000       32.0600           0
1082 A       72    CYS  HG1  HS        0.000000        1.0080           0
1083 A       73    ARG  N    NH1      -0.470000       14.0070           0
1084 A       73    ARG  HN   H         0.310000        1.0080           0
...

Next, we delete the hydrogen atom HG1 at CYS72 (the 1082-th atom) and save it to a new file, say 5vbm-92v-3.X:

$ pdbtop modify -i 5vbm-92v-1.pdb -t 5vbm-92v-2.psf --del-atom 1082 -o 5vbm-92v-3
...
Write PDB: 5vbm-92v-3.pdb
Write PSF: 5vbm-92v-3.psf
Total charge: -5.00000

Now, we have a perfect covalently bonded protein and ligand:

solvate System

Like introduced in Tutorial 1: A Standard Protein, we need to add water to solvate the system, and add ions to neutralize it:

$ pdbtop.exe solvate  -i 5vbm-92v-3.pdb -t 5vbm-92v-3.psf -o 5vbm-sol --box "70 70 70"

The output is:

$ pdbtop.exe solvate -i 5vbm-92v-3.pdb -t 5vbm-92v-3.psf -o 5vbm-sol --box "70 70 70"
...
Building water box: 70.000 x 70.000 x 70.000 Angstrom^3.
12544 water molecules are added.
Add ions:
 Target charge: 0
 Target ionic strength: 0.010 mol/L
5 cations and 0 anions are added.
Final ionic strength: 0.012 mol/L
Write PDB: 5vbm-sol.pdb
Write PSF: 5vbm-sol.psf
Total charge: -0.00000

Now, we have a solvated, neutralized system, which is ready for calculations!