Protein-protein Simulation RMSD, energy scoring, etc – User discussions

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


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