Protein-protein Simulation RMSD, energy scoring, etc

User discussions
1

GROMACS version: 2022.3
GROMACS modification: Yes/No
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I am performing a protein-protein MD simulation, however I am running into an issue such as listed below, where it says “Protein” I can’t distinguish between the two proteins being docked. How would I create an RMSD graphc from the simulation, as well as the solvation energy, binding energy? To get intermolecular force energy, was considering doing a simulation of both proteins docked, then each individual protein simulation and subtracting the values of the intramolecular forces. Also what programs would you recommend?

Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are: 394 Protein residues
There are: 12 Ion residues
There are: 20872 Water residues
Analysing Protein…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…

0 System : 68935 atoms
1 Protein : 6307 atoms
2 Protein-H : 3164 atoms
3 C-alpha : 394 atoms
4 Backbone : 1182 atoms
5 MainChain : 1578 atoms
6 MainChain+Cb : 1956 atoms
7 MainChain+H : 1968 atoms
8 SideChain : 4339 atoms
9 SideChain-H : 1586 atoms
10 Prot-Masses : 6307 atoms
11 non-Protein : 62628 atoms
12 Ion : 12 atoms
13 MG : 1 atoms
14 NA : 11 atoms
15 Water : 62616 atoms
16 SOL : 62616 atoms
17 non-Water : 6319 atoms
18 Water_and_ions : 62628 atoms

2

You need to create index groups for each chain if you want to analyze them separately.

Interaction energy can be computed using energygrps and recalculating the nonbonded energy between the two chains. Note that this quantity is not physically meaningful in most cases.

These quantities require free energy calculations, MM/PBSA, etc.

3

Question. In equilibration, I am unable to see the name of the protein I want to identify. I see during generation of topology, when adding the gro file of one protein in another, I can select the name. How can I list the name of the second protein and its amino acid residue?

4

I want to analyze the proteins interactions with each other, that’s why I want to distinguish both proteins. It’s being listed as one individual protein

5

As I said before, if you want to distinguish different protein chains, you need to create separate index groups for them with make_ndx. If you’re using a .gro file for this, you can really only select by atom number. .pdb or .tpr files allow you to select by chain, if that information is present in the files.

6

The issue is is use pdb2gmx for both proteins. I distinguish the tool.top files (I rename one to topol1.top) however the.itp file for one protein does not distinguish the protein chain name. Would I be able to set up a time to show you and meet via video chat?

7

Which command am I supposed to distinguish the protein from the other protein?

This

gmx make_ndx -f jz4.gro -o index_jz4.ndx

or this one?

gmx make_ndx -f em.gro -o index.ndx

With both commands, it does not list the options of protein chains, so I manually enter:

r 1 - 169 | r 171 - 395

residue 170 is a MG ion. However I get an error when running this. Gromacs identifies “Protein” in the options listed as both proteins (Basically identifying it as one protein during the “gmx make_ndx -f em.gro -o index.ndx” command. Do I need to distinguish the proteins in this? Because it appears this command is to just do the NVT for both systems.

8

What error do you get?