Membrane Thickeness using GridMAT-MD

GROMACS version: 2019
GROMACS modification: No

Hello All,

I want to perform drug-membrane interaction studies using Gram-negative bacterial membranes. I used CHARMM-GUI to model asymmetric mixed membranes with Lipid A in the upper leaflet and POPE:POPG: TOCL2 in the lower leaflet (representative lipids are shown below). For the average thickness of the membrane analysis, I used GridMAT-MD Perl script (parameters provided below, column-wise) from which, I am getting doubtful values. I cross-checked with the center of mass distance from Phosphates in the upper leaflet and lower leaflet (using gmx distance), which provides satisfactory results. I got excellent ‘Z’ values if use symmetric mixed bilayers (POPE:POPG: TOCL2 in both layers), using the GridMAT-MD Perl script.

How to get proper Z values from GridMAT-MD for my membrane model? Kindly help me to resolve this issue.

Please send me your input .gro and settings files via email. This isn’t a GROMACS issue so I’ll handle it myself. I suspect I know what’s going on but I will need your files.

Thank You for your response, Sir.

The zipped folder contains:

  1. The final frame of the PBC centered ".gro’ file.
  2. GridMAT-MD Perl Script.
  3. Input parameters file.
  4. Results displayed in Terminal.
  5. Output Files.
  6. Topology file.

If I miss something here, kindly inform me, Sir.

Sir, kindly enlighten me, how to tackle this issue, even if I use a different combination of layers in the future.

Thank you so much, Sir.

(Attachment is missing)

Some file extensions are not allow, since they may correspond to very large file. One solution is to upload somewhere the zip file (e.i googledoc, onedrive, etc), generate a link and add the link in the post.
Thank you in advance

Kindly consider this. TIA

The issue is the length of the ECLIP and TOCL2 residue names. The script is designed for 4-character residues that are typical of phospholipids. I will have to work on fixing this bug but to circumvent the problem, replace these residue names with ECLI and TOCL in the .gro file and GridMAT-MD parameter file and the calculation will run properly.

Thank you so much, Sir.
Your answer really helped to solve the issue.