DOUBT REGARDING DELTA G BINDING

[Raj Choudhary]

Dear Sir

I carried out a MMGBSA calculation using the trajectory file of a 100ns MD simulation for a protein-ligand complex. I considered frames 1 to10001 at an interval of ten frames. I am attaching my input file (mmpbsa.in), results.dat and results.csv files.

I plotted the delta energy term (Total) (along the Y-axis) as obtained from the result.csv file versus number of frames (along the X-axis); the tif file of the plot is attached. I named the Y-axis as "delta G binding". Is it correct to name the Y-axis as "delta G binding"? If not, then what would be appropriate term that may be used here?

Also if you may please help me to understand that how to include the entropy corrections into my calculation or is it an inbuilt correction and we do not need to do anything extra. 

Thank you in advance

Warm regards

Raj Choudhary
Post Graduate Student
Department of Chemistry
Calcutta University

[marioe911116]

I plotted the delta energy term (Total) (along the Y-axis) as obtained from the result.csv file versus number of frames (along the X-axis); the tif file of the plot is attached. I named the Y-axis as "delta G binding". Is it correct to name the Y-axis as "delta G binding"? If not, then what would be appropriate term that may be used here?

-Technically, the correct name will be "Enthalpy" or "Effective binding free energy" 

Also if you may please help me to understand that how to include the entropy corrections into my calculation or is it an inbuilt correction and we do not need to do anything extra. 

-check this tutorial (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Entropy_calculations/Interaction_Entropy/) under the "Entropy calculations" section in the docs

[Raj Choudhary]

Thank you Sir for your reply. Can we merge the Interaction Entropy Calculations and Enthalpy calculations in a single job for a given protein-ligand complex? If so, what would the input file be like? Or do we need to perform these calculations separately?

Warm regards

Raj Choudhary
Post Graduate Student
Department of Chemistry
Calcutta University

--
You received this message because you are subscribed to a topic in the Google Groups "gmx_MMPBSA" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/gmx_mmpbsa/dXP82BNf0IU/unsubscribe.
To unsubscribe from this group and all its topics, send an email to gmx_mmpbsa+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/d45d3bb1-ef04-41f8-8314-29ea90aedfc0n%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[marioe911116]

Yes, you can obtain both, the enthalpy and the entropy, in a single calculation... you can check the tutorial (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Entropy_calculations/Interaction_Entropy/) for more details on the input file content to do so...

[Raj Choudhary]

Dear Sir

Thank you...Can you kindly go through this attached input file that intends to compute the enthalpy and the entropy from the outputs of 100ns MD simulation of a protein-ligand complex, from 1st frame to 10001th frame with an interval of 10 frames, at 300K? To achieve this, I have set the following parameters:  

interaction_entropy  = 1                                             
ie_segment           = 100 
igb                  = 2

I have highlighted these parameters in the input file.

I am confused regarding the igb to be used for this enthalpy + entropy combined calculation (2 or 5 or something else). 

I will be extremely grateful if you may rectify if I have made any mistake at any point. 

Another question is when do we consider the C2 entropy ?

You received this message because you are subscribed to the Google Groups "gmx_MMPBSA" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gmx_mmpbsa+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/0985ef6a-eb00-4abe-bd55-82507377c186n%40googlegroups.com.

[Mario Ernesto]

The input file looks fine to me... IGB=2 should be fine... C2 is just another approximation to calculate the entropy... Although C2 is slightly more numerically stable than the interaction entropy, it tends to give higher values of entropy...

[Raj Choudhary]

Thank you so much for the guidance.

Is there any specific guideline regarding the IGB value to be set depending on the system to be studied or the nature of calculation to be done?

Since in the tutorial for the interaction entropy (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Entropy_calculations/Interaction_Entropy/) IGB=2, for the C2 entropy (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Entropy_calculations/C2_Entropy/) IGB=5, for only enthalpy (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Protein_ligand/ST/) IGB=5. It's apparently a bit confusing.

Warm regards

[Mario Sergio Valdes]

If you are interested in calculating the IE, please review our documentation at https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/input_file/#entropy-options. Most of your questions and the reference article are specified there.

[Raj Choudhary]

Thank you for the help. Even after reading the reference material as suggested, I am still a bit confused about the IGB number to be set. What appeared to me is that perhaps IGB=5 is an improvised version of IGB=2. So do you suggest using IGB=5 (for enthalpy+entropy calculations?) Or is there any specific guideline?

Pardon me for my ignorance and please correct me if I am wrong.

Warm regards

To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/e0244abc-d5f6-4c43-b929-2e38727899f2n%40googlegroups.com.

[Mario Sergio Valdes]

In principle, the electrostatic component is related to the solvent model, so using different GB models should give different (though presumably close) results. Choosing one or the other depends on several factors, among them, which one is described with better results in the literature for systems similar to yours. Since the EI is calculated from the ΔGgas which includes the electrostatic component, selecting one or the other model, you might get slightly different results. Therefore, you should check which one the author of that method used and check if you get consistent results.

[Raj Choudhary]

Thank you so much for your valuable guidance and sorry for the late reply.

Best regards

To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/75984cd7-67fb-4bc7-a3e5-10f10f882fe0n%40googlegroups.com.