Molecular Dynamics of Protein - Ligand complex on Gromacs Part-1 Preparation of Protein topology

Gromacs molecular dynamics for beginners step by step tutorial. gromacs md simulation based on MDTutorials.com. gromacs lysozyme tutorial with CHARMM36 all-atom force field. Link to MacKerell lab website - mackerell.umary...
Gromacs: • Gromacs - Molecular dy...
playlist - useful computational chemistry and bioinformatics softwares
• How to install Schrödi...
playlist - gromacs procedures for beginners
• How to install Gromacs...
playlist - autodock molecular docking
• How to install Autodoc...
playlist - pymol tutorials
• How to Analyze Autodoc...

[@wifiri]

Muchas gracias... Pero a mi me aparece Fatal error:
"atom c1 not found in building block 1 MET while combining db and rtp" Espero y pueda ayudarme con este problema. Saludos.

[@studywithamisha9903]

Plz make a video on zn dependent mmp protein topology ....

[@mantibiswas2307]

Thank you

[@harshbaid2404]

There is a HETATM called FES(short for Fe2S2) in my pdb file (3GCF)which I cannot remove because it present in the enzyme pocket and has role in enzyme function. But gromacs cannot read it as it is not standard.
Fe2S2 is held by a 2 cystine residues and 2 histidine residues . What can I do to make gromacs read this molecule and continue making the topology file.

[@user-bf8ti6ci9k]

Thank you for your video tutorials! I'm new in MD method, but in our research this method is necessary.
Could give me recommendation about installation of amber force field (ff14sb) in gromacs (version 2022.3), please? The amber tutorials are difficult-to-understand about installation ff on gromacs.
Thank you!

[@mandiraperera7396]

Hi, can u tell me how solve, when adding ions step, error 1( file lig.itp, line 20): atomtype NPYD not found... im in a trouble in my research. This cant be solve to me😢

[@ruchibaliyan7538]

How to make a complex. Pdb file if ligand and protein are already separate

[@pymolbiomolecules]

You have to do molecular docking of that protein with ligand. Then continue the molecular dynamics process with result protein-ligand complex file.

[@Sciinsights]

When i start ligand. Pdb file that is prepared it is empty what i do now
Because it is empty so further ligand.pdb file is converted into mol2. File please suggest me what to do now

[@pymolbiomolecules]

Pls check the ligand code in the command and pdb file is same and try again

[@Sciinsights]

@@pymolbiomolecules this issue is solved now i face error in preparation of ligand topology
When give command "python3 cgneff charm2gmx jz4"

[@amrabbas4679]

Hello, would you tell me how to simulate homodimer and heterodimer protein-ligand complex gromacs please ? Thanks in advance? you can provide me a source as well.

[@user-xe2ll7kz9z]

I edited the 3HTB pdb file, as the tutorial mentions.
Specifically, i run:
1) grep JZ4 3HTB_clean.pdb
2) grep -v HETATM 3HTB_clean > 3htb_processed.pdb
3) gmx pdb2gmx -f 3htb_processed.pdb -o 3htb_processed.gro
Then i choose CHARMM all-atom force field (which i downloaded and extracted to /gromacs/share/gromacs/top/) according to the tutorial, but i keep getting Fatal Errors such as:
Fatal error:
atom C1 not found in buiding block 1MET while combining tdb and rtp
Fatal error:
Atom type H1 (residue MET) not found in atomtype database
Fatal error:
Residue 'HID' not found in residue topology database
I keep editting atomtypes.atp and aminoacids.rtp at the specific force field, but i wonder what am i doing wrong.

[@user-xe2ll7kz9z]

I got a response from gromacs forum and solved my problem!
"The tutorial uses a slightly older version of the CHARMM36 port that did not have a certain terminal patch that screws up methionine. You need to interactively select the NH3+ terminus type with -ter added to the pdb2gmx command."

[@albinjoshi856]

@@user-xe2ll7kz9z can u explain this step, I also have been facing similar problem

[@user-xe2ll7kz9z]

@@albinjoshi856 it's not your fault if you follow the steps. The force field version is older than the time that the tutorial was up. Try adding -ter at the end of the command and inform us please

[@albinjoshi856]

@@user-xe2ll7kz9z is the code supposed to be
gmx pdb2gmx -f 3HTB_clean.pdb -o 3HTB_processed.gro -ter NH3?

[@user-xe2ll7kz9z]

@@albinjoshi856 try this command you wrote without nh3

[@mustaphaelmardi8105]

Thank you for your video tutorials, can you tell me how solve this problem .
program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 790)
Fatal error:
Atom HG in residue SER 1 was not found in rtp entry SER with 13 atoms
while sorting atoms.

[@pymolbiomolecules]

In which command the error occurred

[@pymolbiomolecules]

The error you’re encountering in GROMACS suggests that there is a mismatch between the atoms defined in your PDB file for residue SER 1 and the expected atoms in the corresponding rtp entry for the SER residue. This can happen if the PDB file has an atom that is not recognized by the force field or if there’s a different protonation state expected.
Here are some steps you can take to resolve this issue:
Check the PDB File: Ensure that the atom names in your PDB file match those expected by the force field you are using.
Protonation States: Consider if the protonation state of your residue might be different. You may need to adjust the protonation state to match the force field’s expectations.
Hydrogen Atoms: If the issue is with a hydrogen atom, like HG, it might have been added or named differently in the N-terminus. You might need to remove this hydrogen or rename it according to the rtp entry.
Force Field Compatibility: Make sure that the force field you are using has the appropriate rtp entry for the residue in question. If necessary, you may need to create or modify the rtp entry to include the atom.

[@user-pc3dn3zj6i]

Is we can use this gromacs software in windows 10

[@pymolbiomolecules]

Yes, you can use in windows 10 and windows 11 by compiling with visual studio build tools.

[@NandhaKumar-dp5to]

bro part 2 is available now?

[@pymolbiomolecules]

Yeah bro check description for playlist 👍

[@NandhaKumar-dp5to]

@@pymolbiomolecules got it bro, thanks

[@nandhiniphysics299]

Can you share the video for Opls aa force field

[@pymolbiomolecules]

Yeah i will try to make it, just change the force field to opls in force field selection 👍

[@rahulvishvkarma5852]

Can you perform MD simulation for me. You will be compensate for the same.

[@pymolbiomolecules]

Ohh sry, I don't have powerful enough system to do it for more nanoseconds.