Membrane protein error

[maral afshinpour]

Dear All,

I did md simulation with gromacs and all the input files where prepared with charmm-gui membrane builder. Now I want to show the binding affinity between receptor (r 37-576) and ascorbic acid (r 653). and now after running this command :  gmx_MMPBSA -O -i mmpbsa.in -cs step7_1.tpr -ci ascorbic.ndx -cg 25 26 -ct new_nojump_trans_mol.xtc -o FINAL_RESULTS_MMPBSA.dt -eo FINAL_RESULTS_MMPBSA.csv -cp topol.top              Please find all the required files and error file attached. Thanks for your assistance.

[maral afshinpour]

[maral afshinpour]

On Monday, October 16, 2023 at 12:05:16 PM UTC-5 maral afshinpour wrote:

[maral afshinpour]

[maral afshinpour]

[Mario Sergio Valdes]

You are using gmx_MMPBSA v1.4.1, which is an old version. Please update gmx_MMPBSA to v1.6.2 and try again. If the error persists, please let me know.

[maral afshinpour]

Hello,

I successfully updated gmx_MMPBSA for the analysis, but I'm facing issues interpreting the results. The analysis involved a membrane protein complex with vitamin C as the ligand inside a transporter. I aimed to determine the binding affinity between vitamin C and the protein. However, the calculated electrostatic energy appears lower than expected. This discrepancy raises doubts about the parameters used in the mmpbsa.in file.

Additionally, I lack familiarity with gmx_MMPBSA_ana for result visualization, and I'm not well-versed in programming. Is there an alternative method to interpret these results? I've attached the results along with the required files in my previous email for your reference.

Thank you for your assistance.

Best,

Maral

[maral afshinpour]

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[gmx_MMPBSA]

Please read carefully the docs about protein-membrane calculations as they require a little bit more work:

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Protein_membrane/

There is a box called "Comments on parameters for implicit membranes" where you will find pretty much all related to parameters for calculations involving implicit membranes.

Regarding gmx_MMPBSA_ana, there are some video tutorials that might help:

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/analyzer/

hope this helps...

[Abdul Majeed Khattak]

Hello everyone one I am beginning in Molecular Dynamic Simulation. Could anyone provide me a complete tutorial that you have run to install Amber successfully as I have tried but couldn't gets successful.

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[Mario E. Valdes-Tresanco]

This group is intended to provide feedback on gmx_MMPBSA. Amber mailing list are more suitable for questions related to Amber installation, file processing and so...

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