Very high positive del G value

[Raj Choudhary]

Dear Sir

I am dealing with a dipeptide complex ( a homodimer) which belongs to the category of Intrinsically Disordered Proteins. 1 micro second production MD simulation was done using CHARMM 36 force field on GROMACS.

For MMPBSA calculation (using gmx_MMPBSA v1.6.3),  I am getting a very high positive value for the del G as the -TdelS (corresponding to interaction entropy for the last 25% of the frames) is highly positive. In the input file, PBRadii=7, ipb=2, radioopt=0 were used. Please refer to the attached files for the trajectory xtc, tpr, index files, edr file, result files.

The command used was follows:

gmx_MMPBSA -O -i mmpbsa.in -cs md_protein.tpr -ct md_protein_monomer_center.xtc -ci index.ndx -cg 18 19 -cp protein.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -do FINAL_DECOMP_MMPBSA.dat -deo FINAL_DECOMP_MMPBSA.csv  

Here groups 18 and 19 refer to the two chains in the dimer protein.

Can you please help me to know if there is a way to get a negative value for the del G ? Are there any wrongly attributed parameters in the input file for MMPBSA ?

Thank you

Best regards

Raj

 FINAL_RESULTS_MMPBSA.dat

 gmx_MMPBSA.log

 index.ndx

 md_protein.edr

 md_protein.tpr

 md_protein_monomer_center.xtc

 mmpbsa.in

[marioe911116]

Interaction entropy is not a good fit for your system as it has been reported that it diverges drastically when it is not stable (presumably the case here given that it is a disordered protein).

more info here: https://pubs.acs.org/doi/full/10.1021/acs.jctc.1c00374

[Raj Choudhary]

Sir, can you suggest that what form of entropy can we calculate in this case?

Best regards

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[marioe911116]

Normal modes is implemented in gmx_MMPBSA, however, given the system you have and how long the trajectory is, I am not sure if it is going to be a good fit either... 

[Raj Choudhary]

Thank you Sir. Let me try out the Normal modes of entropy calculation and check the results.

Best regards

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