[gmx-users] Issues combining protein and membrane file?

[Sanim Rahman]

Hi all,

I am trying to prepare a system for a MD simulation of an ion channel
(Kv1.2) in a POPC lipid bilayer. I am struggling inserting the protein into
the lipid membrane. I am currently trying the inflategro.pl approach done
in the KALP15 tutorial. The first step with the prepared structural files
was to combine them together using

cat protein.gro lipid.gro > system.gro

However, after combining them and loading them into VMD, my system has
become distorted and only 151 atoms out 90131 atoms were read. Is there
anything I can do to fix this issue?

I believe it may have to do with the nomenclature of my script. The .gro
file for my protein and lipid bilayer is not written in a consistent format:

  421THR     CA10936   4.791   7.926   7.910
  421THR     CB10937   4.822   7.797   7.831
  421THR    OG110938   4.862   7.831   7.698
  421THR    HG110939   4.882   7.748   7.647
  421THR    CG210940   4.701   7.705   7.826
  421THR      C10941   4.754   7.892   8.055
  421THR     O110942   4.772   7.974   8.146
  421THR     O210943   4.649   7.808   8.074
    1POPC    C1    1   5.168   4.220   4.016 -0.2491  0.0715  0.4836
    1POPC    C2    2   4.942   4.276   3.936  0.1967  0.1087 -0.5850
    1POPC    C3    3   5.108   4.444   3.993  0.3211  0.0553 -0.2150
    1POPC    N4    4   5.085   4.311   3.935  0.2251  0.0126 -0.0777
    1POPC    C5    5   5.129   4.301   3.795 -0.0894 -0.4945 -0.1460
    1POPC    C6    6   5.280   4.304   3.767  0.0019 -0.2403  0.3568
    1POPC   OS7    7   5.354   4.422   3.799  0.0579 -0.0618 -0.4147
    1POPC    P8    8   5.512   4.403   3.778  0.1576  0.2198  0.0575
    1POPC   OM9    9   5.532   4.289   3.686  0.1757 -0.1049  0.4662
    1POPC  OM10   10   5.597   4.524   3.785  0.1671  0.2024  0.2449
    1POPC  OS11   11   5.526   4.331   3.921  0.4792 -0.0093 -0.0879

I updated the number of atoms in my system and removed nonessential lines
as well. Also, would the inflategro procedure be appropriate for this
simulation considering that I am inserting a +10,000 atom protein into a
lipid membrane?

Regards,

*Sanim Rahman*