Membrane Thickeness using GridMAT-MD

User discussions
1

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.

RG-1
RG-11920×1080 133 KB

RG-2
RG-21920×1080 152 KB

RG-3
RG-31616×1405 158 KB

2

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.

3

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 Try1.zip is missing)

6

Hi,
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
Alessandra

7

Kindly consider this. TIA

8

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.

9

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