[Question]: unable to understand the results

[suruchi-25]

My Question is...

i have obtained the .dat and .csv file bt not understanding how to compile the results?

[Valdes-Tresanco-MS]

Please, check this page

[suruchi-25]

I have obtained this result but not getting the results same as it. can you please help

On Sun, Jul 14, 2024 at 4:46 AM Mario Sergio Valdés Tresanco < @.***> wrote:

Please, check this page https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/output/

— Reply to this email directly, view it on GitHub https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/518#issuecomment-2227134569, or unsubscribe https://github.com/notifications/unsubscribe-auth/BI7VTHXMG7LC4KS6QO3SLV3ZMGYLJAVCNFSM6AAAAABK2F44Q2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRXGEZTINJWHE . You are receiving this because you authored the thread.Message ID: @.***>

[Valdes-Tresanco-MS]

Please, attach the result via GitHub since responses via email did not include the attachment

[suruchi-25]

LIG2_FINAL_RESULTS_MMPBSA.csv here i am attaching the file.. please give the solution

[Valdes-Tresanco-MS]

Well, you can get a summary result in the .dat file, which is explained in the documentation. In this file you share, as you can see, the first line (1A) is the method used, in this case, GENERALIZED BORN. If you check the introduction in the documentation, Figure 1, you can see the thermodynamic cycle. So, in the file first, the Complex Energy Terms have one value for every energy term per frame. After that, you can find the receptor, ligand, and delta energy terms, with the same structure as the complex. The energy that permits to prediction if the interaction is favorable or not, is the delta since this value is the rest of the complex minus the sum of its components. Note that the .dat file contains the average for all the computed frames. Please, review the introduction to get close to the algorithms used in gmx_MMPBSA

[suruchi-25]

we need to calculate it manually?

[Valdes-Tresanco-MS]

No. This is the default output file which is always generated and it is a summary of the calculation. With this file, you can see what happeng in the calculation. All the terms are represented by the average, SD, etc. The csv files (they are optional, and must be defined as -eo file_name) contains the information of all energy terms per frames that you can visualize in the gmx_MMPBSA_ana.

[suruchi-25]

Not able to understand from the tutorial video available on the main site, how to analyze from the gmx_MMPBSA_ana. Is any other tutorial video is availabe of using the ana programm