normal Protein-ligand complex

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2 months 6 days ago #8056 by maryam
Protein-ligand complex was created by maryam
Dear all,

I am trying to perform CG-simulation for a protein-ligand complex. I have the CG.itp and pdb files for the protein generated by martinize.py and I also got the .itp file for the ligand from the martini website but I can not continue with the simulation without the CG.pdb file of ligand. I tried to build my own pdb file following a suggestion on mapping I found on this forum but it did not work. The energy minimization step keeps failing. Can anyone help please?/

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2 months 6 days ago #8057 by riccardo
Replied by riccardo on topic Protein-ligand complex
Hi,
How does your ligand look like? Lipid, ring-like, etc? Usually, if you start with a not-even-that-great guess structure, Martini is robust enough to manage to energy minimize it.

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2 months 5 days ago #8058 by maryam
Replied by maryam on topic Protein-ligand complex
My ligand is heme so I will say its ring-like
I get this message when i run the energy minimization:
Energy minimization has stopped, but the forces have not converged to therequested precision Fmax < 10 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was toosmall, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters.Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics.You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file
Thanks.

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2 months 5 days ago #8059 by peterkroon
Replied by peterkroon on topic Protein-ligand complex
A former colleague of ours made a tool that might help. It basically performs an energy minimization from a starting structure where all beads are on a line:
github.com/mnmelo/molmaker

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2 months 5 days ago #8060 by maryam
Replied by maryam on topic Protein-ligand complex
My ligand is heme so I will say its ring-like.
I get this message when i run the energy minimization:
Energy minimization has stopped, but the forces have not converged to therequested precision Fmax < 10 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters.Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics.You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file
Thanks.

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2 months 5 days ago #8061 by maryam
Replied by maryam on topic Protein-ligand complex
HI,
Thanks , I will check this out.

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