Decomposition analysis

e khodayar

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Feb 20, 2024, 11:52:56 AM2/20/24

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Hello,

I have performed per residue decomposition analysis with MMPBSA and MMGBSA. What I did is right or I have to do decomposition analysis just with MMGBSA?

The results that I got with MMPBSA: there are residues with very high energy, even to -100kcalmol-1, while PB binding is only -17kcalmol-1?

This my input file:

&general
startframe=8000, endframe=10000, verbose=1, interval=5,
interaction_entropy=1, ie_segment=50,temperature=300
/
&pb
ipb=2
/
&decomp
idecomp=2, dec_verbose=3,
print_res="within 10"
/

I upload output results.

PB_NORMAL_PB_Delta_TDC-10.csv

gmx_MMPBSA

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Feb 20, 2024, 2:18:45 PM2/20/24

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PLease, upload the entire CSV and .dat files to chek the results

Message has been deleted

Mario E. Valdes-Tresanco

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Feb 21, 2024, 12:55:32 AM2/21/24

to e khodayar, gmx_MMPBSA

could you please submit the csv from the decomposition analysis

On Tue, Feb 20, 2024 at 10:42 PM e khodayar <e.khod...@gmail.com> wrote:

Thank you for reply
I upload my .csv and .dat

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e khodayar

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Feb 21, 2024, 12:56:38 AM2/21/24

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Thank you for reply

I upload .csv and .dat files

On Tuesday, February 20, 2024 at 11:18:45 AM UTC-8 gmx_MMPBSA wrote:

FINAL_RESULTS_MMPBSA.csv

FINAL_DECOMP_MMPBSA.dat

Mario E. Valdes-Tresanco

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Feb 21, 2024, 1:03:18 AM2/21/24

to e khodayar, gmx_MMPBSA

I need the FINAL_DECOMP_MMPBSA.csv file

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e khodayar

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Feb 22, 2024, 1:05:16 AM2/22/24

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I upload this files

FINAL_DECOMP_MMPBSA.dat

FINAL_RESULTS_MMPBSA.csv

gmx_MMPBSA

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Feb 22, 2024, 2:27:16 PM2/22/24

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During a decomposition calculation, you can generate 4 files, FINAL_RESULTS_MMPBSA.data, FINAL_RESULTS_MMPBSA.csv, FINAL_DECOMP_MMPBSA.dat, and FINAL_DECOMP_MMPBSA.csv. I need the FINAL_DECOMP_MMPBSA.csv

e khodayar

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Feb 24, 2024, 8:28:47 AM2/24/24

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During a decomposition calculation, just 3 files generated, FINAL_RESULTS_MMPBSA.data, FINAL_RESULTS_MMPBSA.csv, FINAL_DECOMP_MMPBSA.dat. FINAL_DECOMP_MMPBSA.csv is not generated. I upload FINAL_RESULTS_MMPBSA.data, FINAL_RESULTS_MMPBSA.csv, FINAL_DECOMP_MMPBSA.dat files.

FINAL_RESULTS_MMPBSA.dat

FINAL_RESULTS_MMPBSA.csv

FINAL_DECOMP_MMPBSA.dat

gmx_MMPBSA

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Feb 24, 2024, 5:45:42 PM2/24/24

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Use this command to generate all the output files:

gmx_MMPBSA --rewrite-output -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -do FINAL_DECOMP_MMPBSA.dat -deo FINAL_DECOMP_MMPBSA.csv

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