<< PDBWriter parameters >>

[I. Camps]

Hi,

I am using the following code to export my trajectory as a multi-model PDB file:

complexx_temp = u_aligned.select_atoms(sel_prot, sel_lig)
with MDAnalysis.Writer("out_" + fname_root + "_PDBtrajectories.pdb", bonds=None, multiframe=True) as W:
    for ts in u_aligned.trajectory:
        W.write(complexx_temp)

Then, I use PLIP to calculate the interactions between the ligand and the protein.

The problem here is that the PLIP program is complaining about the PDB final format.

My DCD/PSF files have the complex system information as segment IDs (PROA/HETA) chains (A for protein, B for ligand), residue names (protein ok, and LIG for ligand).

The PDB output from MDAnalysis (v2.6) is in the form:

TITLE     MDANALYSIS FRAMES FROM 0, STEP 1: Created by PDBWriter
CRYST1  144.632  144.632  144.632  90.00  90.00  90.00 P 1           1
MODEL        1
ATOM      1  N   MET X   1     -28.647 -45.944  26.553  1.00  0.00      PROA    
ATOM      2  HT1 MET X   1     -29.677 -46.064  26.469  1.00  0.00      PROA    
... 

ATOM   8953  H20 LIG X 999     -57.268 -41.180   4.867  1.00  0.00      HETA    
ATOM   8954  LP1 LIG X 999     -65.187 -35.766   2.503  1.00  0.00      HETA    

Is it possible to check/fix this PDB output by adding the information already present in the DCD/PSF files?

Thanks in advance.

Camps

[Rocco Meli]

Hello,

as per our recent post we are trying to move to GitHub Discussions: https://groups.google.com/g/mdnalysis-discussion/c/Uj1_ajtPa5Y

The mailing list is still open but mainly to finish off already started discussions. Would you ming re-posting this question in GitHub Discussions: https://github.com/MDAnalysis/mdanalysis/discussions

Many thanks,

Rocco

[I. Camps]

Hey Rocco.

Thank you for the information. I already post in Github.

[Rocco Meli]

Thank you! I replied to you there.

Best,

Rocco