I had done simulation of my protein-ligand complex and generated the attached potential energy graph. I need to know if my graph is correct and if not what should I do to improve/correct my results.
if the protein-ligand system is stable and you have treated the protein ligand complex as single entity, then this graph of P.E. is wrong..use the manual to correctly run the commands...or else you have done something wrong in running the simulation correctly..
After docking I have followed the GROMACS tutorial available online for protein-ligand complex in which I have used GROMOS96 force field.
I have generated the ligand topology from PRODRG website.
In mdp files I have increased the minimisation steps to 500000 steps.
Pls paste your minimization mdp file. Was the minimization after solvation with ions ?
@Agnivo Gosai. Yes the minimisation was after solvation of ions. following is my mdp files i used before running mdrun.
@tanuj sharma... I have followed the web tutorial and used mdp files provided in the link as is. How shud i find out if my system is stable? I have docked the ligand with protein and then performed simulation.
Do you use both the files attached for EM on the structure ? What is the force field used by you? List all steps clearly starting from topology preparation to EM, step by step.
What warnings / error messages do you find during all these steps?
Following are the steps I performed:
1. I docked the protein ligand using autodock and saved the complex in PDB format.
2. Then from the complex i extracted the ligand coordinates and prepared topology and .gro files for ligand using PRODRG server for GROMOS 96 ff.
3. Converted the protein PDB file to .gro using GROMOS 96 53A4 ff
4. Include the ligand topology file into topol.top file and to molecules section
5. Added ions and solvated the complex and then and then energy minimized using em.mdp file provided in the gromacs tutorial.
6. Generated potential energy graph using g_energy and the resulting graph was as attached above.
Did you not receive any warnings or error messages ? Can you provide a link to the .xvg file generated as the output of g_energy as well as the EM mdrun log file.
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