gmx_MMPBSA: Graph of energy vs frame #

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Ishrat Jahan

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Jan 25, 2024, 2:40:25 PMJan 25
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Dear all,
I have done the MD simulation of the protein-peptide system using the charmm36 force field. After that, I tried calculating the binding free energy between protein and peptide using gmx_MMPBSA and plotted the graph between delta G and frame #. In the plot, the value of delta G is 0 at some frame. What does that indicate? I have applied the PBC on the trajectory but still getting the same results.
Any comments or suggestions regarding this will be highly appreciated.
Thank you

Mario E. Valdes-Tresanco

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Jan 25, 2024, 3:15:24 PMJan 25
to Ishrat Jahan, gmx_MMPBSA
Could you please send the result girl that you load onto gmc_MMPBSA_ana (extension .mmxsa)

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Ishrat Jahan

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Jan 25, 2024, 3:21:23 PMJan 25
to Mario E. Valdes-Tresanco, gmx_MMPBSA
Here it is.
Best Regards
Dr. Ishrat Jahan
Postdoctoral Research Fellow
University of Rhode Island
United States, 02881
COMPACT_MMXSA_RESULTS.mmxsa

Mario E. Valdes-Tresanco

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Jan 25, 2024, 5:24:58 PMJan 25
to Ishrat Jahan, gmx_MMPBSA
Everything looks ok, there seems to be no issues with the processing part, which makes me think it should be related to the trajectory. Could you please send the files you are using?

Ishrat Jahan

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Jan 26, 2024, 11:35:59 AMJan 26
to Mario E. Valdes-Tresanco, gmx_MMPBSA
Yes, sure.
Best Regards
Dr. Ishrat Jahan
Postdoctoral Research Fellow
University of Rhode Island
United States, 02881

On Thu, Jan 25, 2024 at 5:24 PM Mario E. Valdes-Tresanco
mmpbsa.in
v18C_prot_0ns.pdb
v18C_prot_last100ns.xtc

gmx_MMPBSA

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Jan 28, 2024, 12:51:13 AMJan 28
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There are some frames where the two proteins are separated... Please, check the fitting process and make sure the complex is not broken due to periodic conditions...

Screenshot from 2024-01-27 22-49-34.png

Ishrat Jahan

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Jan 28, 2024, 7:15:10 AMJan 28
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I have tried to do but still in some frames I found two protein at different positions. I will again try. Thank you for your time and suggestion.


Best Regards
Dr. Ishrat Jahan
Postdoctoral Research Fellow
University of Rhode Island
United States, 02881
On Sun, 28 Jan 2024 at 00:51, gmx_MMPBSA <gmx_m...@googlegroups.com> wrote:
There are some frames where the two proteins are separated... Please, check the fitting process and make sure the complex is not broken due to periodic conditions...


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nikpekbook

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Jan 28, 2024, 4:35:42 PMJan 28
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Try to process your trajectory. You can use 1) -pbc whole, then 2) -pbc nojump and then 3) -pbc mol -center to keep your proteins together. It may help in some cases.
Option -fit rot+trans may also be helpful.
But the most simple is to create a new index with interface residues of one protein chain. And then use -pbc mol -center - n index.ndx using for centering your new index group. Proteins will keep together.

воскресенье, 28 января 2024 г. в 14:15:10 UTC+2, ishrat...@uri.edu:
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