GROMACS Protein-Ligand complex simulations Troubleshooting
Budget: ₹600 – ₹1,500 INR
I am currently working on protein-ligand complex simulations using GROMACS and have encountered several issues during the ligand topology generation process.
When I attempt to use the CHARMM force field (specifically CHARMM27) for the protein, I encounter errors related to the Python script during ligand topology generation.
The GROMACS tutorial suggests using CHARMM for both protein and ligand, but I am unable to generate a consistent force field topology for the ligand.
I have also tried using the SwissParam force field for the ligand; however, I face compatibility issues. The ligand topology does not match the protein topology due to discrepancies in Lennard-Jones and Buckingham non-bonded interactions.
Additionally, I receive errors indicating "invalid directive for atom types," which further complicates the topology generation process.
Recommendations for resolving the errors encountered with the SwissParam force field, particularly regarding non-bonded interactions and atom type directives. I would appreciate your guidance in resolving these challenges.
Due to high unavailability of high-computing facility, I am unable to perform.
Expert Needed for GROMACS Protein Ligand Complex Simulations".
Proficiency in GROMACS and molecular dynamics simulations.
Familiarity with CHARMM and SwissParam force fields.
Experience in troubleshooting topology generation issues.
I have upload my protein and ligand files for simulations. Can anyone do this simulations and give me the all details?
I have attached my files protein complex for simulations
If anyone, I will give them or two-three complex for simulations.
When I attempt to use the CHARMM force field (specifically CHARMM27) for the protein, I encounter errors related to the Python script during ligand topology generation.
The GROMACS tutorial suggests using CHARMM for both protein and ligand, but I am unable to generate a consistent force field topology for the ligand.
I have also tried using the SwissParam force field for the ligand; however, I face compatibility issues. The ligand topology does not match the protein topology due to discrepancies in Lennard-Jones and Buckingham non-bonded interactions.
Additionally, I receive errors indicating "invalid directive for atom types," which further complicates the topology generation process.
Recommendations for resolving the errors encountered with the SwissParam force field, particularly regarding non-bonded interactions and atom type directives. I would appreciate your guidance in resolving these challenges.
Due to high unavailability of high-computing facility, I am unable to perform.
Expert Needed for GROMACS Protein Ligand Complex Simulations".
Proficiency in GROMACS and molecular dynamics simulations.
Familiarity with CHARMM and SwissParam force fields.
Experience in troubleshooting topology generation issues.
I have upload my protein and ligand files for simulations. Can anyone do this simulations and give me the all details?
I have attached my files protein complex for simulations
If anyone, I will give them or two-three complex for simulations.