calc error for membrane protein mmpbsa calculation

[Imojara Anna]

Hello, I tried running mmpbsa analysis for my protein ligand complex and got the error shown in the attached image. i generated the simulation input files from charmmgui and used charmm forcefield to run the simulation using gromacs. the protein is a membrane protein with seven subunit and i used all subunit for the simulation. for the mmpbsa calculations, i used  a modified version of the input file sample for membrane protein  which i have also attached to this mail. please i will like to know why i am getting this error and also how i can possibly resolve this error. i have also attached some relevant output files for the mmpbsa calculation.

secondly, i want to ask if it is right for me to just calculate the mmpsa for the protein-ligand complex while ignoring the membrane protein parameter especially when the protein ligand interaction did not occur at regions that are within the lipid bilayer.....

Thank you for your response

[muralidhar pandey]

Does the complex have any type of metals,if yes remove its properly,then do 

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[marioe911116]

Hello, I tried running mmpbsa analysis for my protein ligand complex and got the error shown in the attached image. i generated the simulation input files from charmmgui and used charmm forcefield to run the simulation using gromacs. the protein is a membrane protein with seven subunit and i used all subunit for the simulation. for the mmpbsa calculations, i used  a modified version of the input file sample for membrane protein  which i have also attached to this mail. please i will like to know why i am getting this error and also how i can possibly resolve this error. i have also attached some relevant output files for the mmpbsa calculation.

I couldn't identify the error from the files you submitted. Could you send all the files that were produced during the calculation?

secondly, i want to ask if it is right for me to just calculate the mmpsa for the protein-ligand complex while ignoring the membrane protein parameter especially when the protein ligand interaction did not occur at regions that are within the lipid bilayer.....

This is tricky; I will say the best way to prove there is no effect from the membrane is to run PB calculations with and without the membrane parameters (make sure here all the parameters not related to the membrane are the same) and compare; if they are roughly the same, in that case you might use GB since the membrane is not involved in the interaction. After all, this is a post-processing tool, and whatever effect the membrane would have on the conformation is already reflected in the trajectory, and errors in bonded and non-bonded interactions should cancel out. Anyway, I have not tried this myself, and comments from someone who actually tried are welcome