Tutorial 6: Define My Own Modification

In this tutorial, we will show you how to use pdbtop to define your own modification that are not yet supported by pdbtop.

Prepare a RTF File

Assume we want to define a modification called “ethylation” for lysine, we can prepare a file called my.rtf with following content:

my.rtf
 1PRES EL           0.33 !
 2ATOM NZ   NH3    -0.30 !        HF1   HI2
 3ATOM CF   CT2     0.06 !        |     |
 4ATOM HF1  HA      0.09 !    HF2-CF--CF2--HI1
 5ATOM HF2  HA      0.09 !       /       \
 6ATOM CF2  CT3    -0.18 !  CE--NZ--HZ2   HI3
 7ATOM HI1  HA      0.09 !       \
 8ATOM HI2  HA      0.09 !       HZ3
 9ATOM HI3  HA      0.09 !
10GROUP                  !
11DELETE ATOM HZ1        !
12BOND NZ CF CF HF1 CF HF2 CF CF2
13BOND CF2 HI1 CF2 HI2 CF2 HI3
14IC  CD   CE  NZ   CF    1.5350 110.4600  179.9200 110.0200  1.4604
15IC  CE   NZ  CF  HF1    0.0000  0.0000  -173.6500 110.8500  1.1104
16IC  HF1  NZ  CF  HF2    0.0000  0.0000   119.5100 110.4100  1.1109
17IC  HF1  NZ  CF  CF2    0.0000  0.0000  -120.3900 111.1100  1.5300
18IC  NZ   CF  CF2 HI1    0.0000  0.0000  -179.5100 110.4100  1.1109
19IC  HI1  CF  CF2 HI2    0.0000  0.0000   119.5100 110.4100  1.1109
20IC  HI1  CF  CF2 HI3    0.0000  0.0000  -119.5100 110.4100  1.1109

The residue EL defines how to modify lysine to obtain an “ethylated” lysine. In my.rtf, you can define arbitrary number of modifications.

Here we explain how this “ethylation” is realized:

  • Everything after ! is comment.

  • PRES EL           0.33: defines a patch called EL. 0.33 is not used.

  • ATOM NZ   NH3    -0.30: NZ is already defined in LYS (defined in data/top_all36_prot.rtf). This statement modifies atomic type (NH3) and charge (-0.30).

  • ATOM HF1  HA      0.09: HF1 is a new atom. For new atoms, the name can be arbitrary, as long as it is unique within this residue.

  • DELETE ATOM HZ1: Delete atom HZ1 in LYS.

  • BOND NZ CF CF HF1 CF HF2 CF CF2: defines 3 bonds: NZ-CF, CF-HF1, CF-HF2, and CF-HF3.

  • IC  HF1  NZ  CF  CF2    0.0000  0.0000  -120.3900 111.1100  1.5300: defines the coordinate of the last atom in Z-matrix: bond CF2-CF: 1.5300; angle CF2-CF-NZ: 111.1100; dihedral CF2-CF-NZ-HF1: -120.390000.

Do Modification

Assume we have a protein structure 5vbm-4.pdb and its topology 5vbm-4.psf (see Tutorial 1: A Standard Protein), and we want to perform this ethylation for the residue LYS5 at chain A, then we can use the following command:

$ pdbtop modify -i 5vbm-4.pdb -t 5vbm-4.psf -o 5vbm-mod --add-rtfs my.rtf --my-mod "EL 5A"

Here, --add-rtfs lets pdbtop read my.rtf to load user-defined residues or patches, and --my-mod means apply EL to residue 5 at chain A. The result is shown below:

_images/p17.png