Missing files while following the membrane protein tutorial

User discussions
1

Hello Community
I am a beginner in GROMACS and was trying to follow the tutorials on the website. For the membrane protein tutorial, step 2, the link to download the dppc128.pdb, dppc.itp and lipid.itp files is not working.
Can you please help me with alternatives?
(I am not at all familiar with CHARMM-GUI also)
Thanks

2

Hi,
Which tutorial do you refer to? Do you refer to a tutorial hosted at https://tutorials.gromacs.org/?
For example Introduction to Membrane-Protein Simulation — GROMACS tutorials https://tutorials.gromacs.org documentation
Kind regards
Alessandra

3

I am looking at
http://www.mdtutorials.com/gmx/membrane_protein/01_pdb2gmx.html

Thanks
Suchetana

4

Hello,

reporting missing lipid parameters from the webpage

“These lipid parameters are distributed by D. Peter Tieleman, through his website. While you are there, download the following files:

  • dppc128.pdb - the structure of a 128-lipid DPPC bilayer

  • dppc.itp - the [moleculetype] definition for DPPC

  • lipid.itp - Berger lipid parameters“

Because the linked website of Tieleman is not working. Please, provide these missing files.

5

In between I found missing files in GitHub - fuentesdt/MembraneProtein .

6

The author of the tutorials explicitly states that

As of summer 2023, the required Berger lipid parameters are no longer available online. The authors themselves have raised issues of their validity and they are not available. This tutorial will remain online as a reference until I rewrite it. Please DO NOT proceed and expect the tutorial to work. It will not.

7

Well, we do not need exact results from this tutorial, we just need working it somehow, mainly from the technical point of view…