interactions between protein and ligand only ??

[mohamedmarzouk22]

I want to study the interaction between protein and DNA in different conformations, but I am not interested in the interaction between protein residues with other protein residues I am only interested in protein DNA. I am using command like that ; plip -f 1tsr.pdb -vt -o outputfile How can I modify these options to get only protein-ligand (this case it's DNA)

[fkaiserbio]

I don't quite understand your question. In the standard mode, PLIP treats the DNA as a ligand. This results in reporting of interactions between DNA and protein. The following command works for me:

$ docker run --rm \
    -v ${PWD}:/results \
    -w /results \
    -u $(id -u ${USER}):$(id -g ${USER}) \
    pharmai/plip:latest -i 1tsr -yvxt

The documentation describes how to treat DNA as receptor if, additionally, a small molecule ligand is present: https://github.com/pharmai/plip/blob/master/DOCUMENTATION.md#interactions-of-molecules-with-dnarna

[mohamedmarzouk22]

1) The system contains only one chain of protein and DNA!!! 2) I want to study the interaction between them
I got something like that in the screenshot, there is information in the output file about the interaction between two residues from the protein such as ASN and CY2. I am not interested, I am only interested in the interaction between residues from protein and DNA. How to modify the command to do that

[fkaiserbio]

It seems that your structure contains an HETATM entity with three-letter code CY2 in the PDB file. It is recognized by PLIP as a ligand. Please make sure there a no non-standard amino acids in your PDB file, otherwise they will be recognized as ligand. For the original PDB structure there is no such behavior and everything is reported correctly:

**Hydrogen Bonds**
+-------+---------+----------+-----------+-------------+--------------+-----------+----------+----------+-----------+-----------+----------+-----------+-------------+--------------+------------------------+------------------------+
| RESNR | RESTYPE | RESCHAIN | RESNR_LIG | RESTYPE_LIG | RESCHAIN_LIG | SIDECHAIN | DIST_H-A | DIST_D-A | DON_ANGLE | PROTISDON | DONORIDX | DONORTYPE | ACCEPTORIDX | ACCEPTORTYPE | LIGCOO                 | PROTCOO                | 
+=======+=========+==========+===========+=============+==============+===========+==========+==========+===========+===========+==========+===========+=============+==============+========================+========================+
| 120   | LYS     | B        | 7         | DG          | F            | True      | 2.63     | 3.61     | 160.05    | True      | 2584     | N3        | 555         | Nar          | 64.751, 38.448, 85.057 | 61.396, 37.119, 84.977 | 
+-------+---------+----------+-----------+-------------+--------------+-----------+----------+----------+-----------+-----------+----------+-----------+-------------+--------------+------------------------+------------------------+
| 120   | LYS     | B        | 7         | DG          | F            | False     | 2.88     | 3.76     | 150.16    | True      | 2576     | Nam       | 544         | O3           | 66.730, 38.121, 91.364 | 66.109, 34.843, 89.626 | 
+-------+---------+----------+-----------+-------------+--------------+-----------+----------+----------+-----------+-----------+----------+-----------+-------------+--------------+------------------------+------------------------+
| 121   | SER     | C        | 16        | DT          | F            | False     | 2.98     | 3.46     | 111.37    | True      | 4115     | Nam       | 732         | O2           | 40.532, 19.658, 86.253 | 40.382, 16.357, 87.272 | 
+-------+---------+----------+-----------+-------------+--------------+-----------+----------+----------+-----------+-----------+----------+-----------+-------------+--------------+------------------------+------------------------+
| 121   | SER     | C        | 16        | DT          | F            | True      | 2.78     | 3.71     | 161.72    | False     | 731      | O3        | 4120        | O3           | 41.815, 20.250, 88.387 | 42.989, 16.769, 88.908 | 
+-------+---------+----------+-----------+-------------+--------------+-----------+----------+----------+-----------+-----------+----------+-----------+-------------+--------------+------------------------+------------------------+
| 248   | ARG     | B        | 14        | DT          | F            | True      | 3.45     | 3.94     | 112.89    | True      | 3592     | Ng+       | 697         | O3           | 46.840, 25.417, 79.956 | 49.430, 24.302, 82.709 | 
+-------+---------+----------+-----------+-------------+--------------+-----------+----------+----------+-----------+-----------+----------+-----------+-------------+--------------+------------------------+------------------------+
| 248   | ARG     | B        | 14        | DT          | F            | True      | 3.32     | 3.82     | 113.59    | True      | 3593     | Ng+       | 697         | O3           | 46.840, 25.417, 79.956 | 50.539, 25.141, 80.865 | 
+-------+---------+----------+-----------+-------------+--------------+-----------+----------+----------+-----------+-----------+----------+-----------+-------------+--------------+------------------------+------------------------+
| 280   | ARG     | B        | 10        | DC          | F            | True      | 3.48     | 4.02     | 116.95    | True      | 3834     | Ng+       | 624         | Npl          | 54.676, 36.068, 84.058 | 57.551, 33.627, 85.452 | 
+-------+---------+----------+-----------+-------------+--------------+-----------+----------+----------+-----------+-----------+----------+-----------+-------------+--------------+------------------------+------------------------+
| 283   | ARG     | B        | 7         | DG          | F            | True      | 2.96     | 3.53     | 118.24    | True      | 3865     | Ng+       | 544         | O3           | 66.730, 38.121, 91.364 | 64.676, 35.549, 92.647 | 
+-------+---------+----------+-----------+-------------+--------------+-----------+----------+----------+-----------+-----------+----------+-----------+-------------+--------------+------------------------+------------------------+

So obviously this is not a bug by PLIP but an invalid PDB file.