The zero values of Bond, Dihedral, Angle, UB, IMP, and CMAP terms

[Sarthak Trivedi SVNIT]

Respected Sir,

I am posting this query to ask and discuss the reason behind the zero values I am getting in terms of Delta calculations. I am getting zero values in Bond, Angle Dihedral, UB, IMP, CMAP terms. I am not having any idea about it, and if it's right, then what is the logical reason behind it and what can I conclude from these zero values. I am attaching hery data files of two different complexes results. Please analyse it and give some lights on the results through your opinions. 

Thank you so much,

Regards,

Sarthak.

[Mario Sergio Valdes]

What exactly don't you understand? I noticed that you previously answered what it means and why it happens (https://groups.google.com/g/gmx_mmpbsa/c/61J1-UULxsY/m/n8oXHZC_BAAJ). Can you be clear on what you don't understand?

[Sarthak Trivedi SVNIT]

Accept my sincere apology for unclear question. As per last thread I understood that terms were neglected as per single trajectory protocol (as we have considered same bounded and unbounded states of receptor and ligand). off course the multiple trajectory protocol will take these terms into account of binding free energy calculations. the question is how much difference it (MTP) will make in results? Does the extra computational cost will able to make me comment from these (MTP) results ? Because as I am having a good computational resources, I am thinking to perform same calculations with MTP.

Thank you in advance

Regards,

Sarthak 

[marioe911116]

MTP is in theory more accurate as changes in the receptor and ligand upon binding are taken into account; HOWEVER, it tends to give extremely large standard deviations and poorer results than STP (mainly associated with errors due to the force fields).