More than one protein molecule in the box

User discussions
1

GROMACS version: 2021.4
GROMACS modification: Yes/No
Here post your question : In lysozyme-water tutorial, we have one lysozyme molecule in the box. I want to know how to place more than one protein molecules in the box using GROMACS. Can anyone please help me with this?

2

There are two easy options. You can

  • do that manually, by duplicating the protein file, making sure the box is large enough, using gmx editconf to translate/rotate the copied protein, and append the copy to the original, or
  • use gmx insert-molecules to automatically insert any molecule into a preexisting structure (again, make sure your box is large enough to accommodate the other protein(s).

You can do these steps before or after you go through gmx pdb2gmx - if you already have a working topology, just increment the number of protein copies in the [ molecules ] section at the bottom of the .top file. If you go through gmx pdb2gmx, it should automatically create the required number of instances.

3

Can you please help me with the full command for each option?

4

Sure I could, but what’s the problem that you’re facing after asking the tools for -h help?

5

Actually I don’t know how to do it and at what step I should insert the proteins( while creating the simulation box we center the protein in it, but I am confused when I have to insert more than one ). If you could help me know how and when to insert the proteins (I want to insert the same protein molecule, but it should be more in no.), it will be of great help.

6

As I said, you can add the protein (or multiple copies) after creating the topology entry, in which case insert-molecules is the way to go, and you only need to adjust the number of copies at the bottom of the .top file; or, you can insert the copy/copies before creating the topologies (either manually or with insert-molecules), and this way pdb2gmx will spend more time doing the same thing over and over again, but the result will be pretty much similar.

Once you increase your box vectors to the desired size, you can just do

gmx insert-molecules -f single_protein.gro -ci single_protein.gro -nmol 5

and it will insert 5 extra copies of your protein into out.gro, if it can physically fit them.

Again, it’s completely up to you to use the pdb2gmx-processed structure and only adjust the .top, or to use the non-parsed structure and run pdb2gmx on out.gro.

1 Like
7

I did the following steps-

grep -v HOH 1aki.pdb > 1AKI_clean.pdb
gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water spce -ignh
gmx editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic

After the above steps I followed with -
gmx insert-molecules -f 1AKI_newbox.gro -ci 1AKI_processed.gro -nmol 5

So I got an out.gro file. But while viewing in VMD, I can see 5 protein molecules in the out.gro file but only 1 in 1AKI_newbox.gro. Can you please tell me why is that and which file (out.gro or 1AKI_newbox.gro) should i use for the next solvation step. Kindly help me with this.

8

That’s why I suggested to read through the -h option first:

Options to specify input files:

 -f      [<.gro/.g96/...>]  (protein.gro)    (Opt.)
           Existing configuration to insert into: gro g96 pdb brk ent esp tpr
 -ci     [<.gro/.g96/...>]  (insert.gro)
           Configuration to insert: gro g96 pdb brk ent esp tpr
 -ip     [<.dat>]           (positions.dat)  (Opt.)
           Predefined insertion trial positions
 -n      [<.ndx>]           (index.ndx)      (Opt.)
           Extra index groups

Options to specify output files:

 -o      [<.gro/.g96/...>]  (out.gro)
           Output configuration after insertion: gro g96 pdb brk ent esp

Both -f and -ci specify input files. The output file is, by default, called out.gro (of course you can overwrite the default if desired).

To proceed, you’ll need to edit your topology to accommodate the extra copies of the protein, but aside from this, of course, use the output of insert-molecules.

Also, if you only see 5 copies of your protein in the output, you might need to make the box larger or increase -try, because you had 1 copy to start with and then asked to add 5 more.