Simulation of protein in lipid using files from charmm gui in gromacs

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1

GROMACS version: latest
GROMACS modification: Yes/No
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Hello,
I am simulating a protein in lipid bilayer (DMPC) and have generated files using charmm gui input generator.
after extracting the input files I can see 6 equilibration mdp files that is step6.1_equilibration.mdp to step6,6_equilibartion.mdp

  1. Do i have to run all the equilibration step before production run?
  2. How can i get the phi and psi value for plotting Ramachandran plot (is it by using gmx rama command)? and also I want to plot it residue wise how can i accomplish that?
  3. I have earlier simulated one peptide with Alternating L and D amino acid but after md run i could see one that one D-Ala is totally in the second quadrant that is phi (-) and psi(+) is it possible to have D amino acid in second quadrant of ramachandran plot?
    if yes in the 3rd question what can we infer from the result?

Thanks in advance
Hoping for a quick reply

3

Hi,

Do i have to run all the equilibration step before production run?

I do not know exactly which steps are suggested by charmm gui, but
I suggest to understand the meaning of each step before running it by looking at the mdp file.

In general, before data production, the following is important

  • energy minimization to have the system in one of the energy minima of the potential used to describe the system (force field) and to remove sterical clash
  • relax the environment (solvent and ion and lipid bilayer) around the protein to avoid bad contact (usually this step is done applying position restraint to the hetero atoms of the protein)
  • equilibrate the system to the desired temperature and pressure,

Once the system is relax and equilibrate in the corrected thermodynamic ensemble, you can start data production.

best regards
Alessandra

4

Thanks you so much

5

Can some one address question 2 and 3?

6

gmx rama is the right tool

From the help description: " Using simple Unix tools such as grep you can select out specific residues."

It sounds like the stereochemistry inverted. It should be apparent by simple visualization if it did. Sometimes this can happen during minimization if the Hα position was not generated well.

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for 3 so how to overcome such kind of problem if during minimization the H alpha is not generated well?

8

Is that actually an issue? Should be visually obvious. If it is, then rebuild the H or use dihedral restraints to reposition it.

9

Sorry for late reply ,

How should I rebuild the H or use dihedral restraints to reposition it, can you please elaborate a bit ? What’s the protocol ?

Can I rebuild H after my md run is finish ??

(- I had used define DDIHRES in mdp files except production files )

10

I am attaching a drive link here in which there is a screenshot of DALA-6 ramachandran plot and there you can see some dihedral angle come in second quadrant and some in 3rd which is not allowed region for D aminoacid.

and in gromacs files that i have attached there are all files including initial structure, mdp files that i have generated by charmm gui.
link- check - Google Drive

please have a look and do comment if something seems wrong

11

Can any one please help?

12

This one

13

I don’t know what the issue is and I’m afraid it’s not something I have time to dig into in detail. If the stereochemistry is inverting anywhere, you should be able to identify when that happens visually and work backwards from there to determine where the problem might lie.