regarding positive binding energy

[Joytisha Basantia]

Dear MMPBSA Support Team,

I am dealing with a protein-protein complex. 100 nano second production MD simulation was done using the OPLS force field on GROMACS.

I am getting a very high positive value for the del G. Here groups 19 and 21 refer to the backbone of both proteins (one as receptor and another as ligand).

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 ?

[mariosergi...@gmail.com]

It's difficult to know what the problem might be if we don't have the minimum information. Consider attaching the gmx_MMPBSA.log file. At the very least, make sure you're selecting the correct groups that contain the receptor and ligand.

[Rahman Fadhlu]

 Hi Joytisha

Positive delta G value means your proteins do not bind.
How about your docking binding energy?

If your docking's binding energy value is "negative" and the gmx_MMPBSA's free energy is "positive", means the parameter during MDS might need to be looked at.   

[mariosergi...@gmail.com]

You must select all atoms, not the bb