NAMD+MM_GBSA/PBSA

[臧敏]

Hi everynone,

     For the NAMD version of trajectory MM_GBSA/PBSA calculation, I used gmx_MMPBSA/example/psf_dcd/protein_protein for testing (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/psf_dcd/protein_protein/) , but I found that when adding &decomp (idecomp=2, dec_verbose=3, print_res="within 100" ), the energy decomposition of all C-termius  backbone of the amino acids is 0, I think this is very abnormal, so I have doubts about the overall energy calculation, has anyone met this problem, how should I solve it? Thanks a lot.

Best wishes,

Besty

[marioe911116]

Could you please share the results files?

[臧敏]

Here are the result files that I got[&decomp (idecomp=2, dec_verbose=3, print_res="A/1-223 B/1-57" )]. The all origin files are here (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/psf_dcd/protein_protein/) and the all files are too big that I cannot upload. Thanks a lot.

Best Wishes,

Besty

 

 

 

------------------ Original ------------------

From:  "marioe911116"<marioe...@gmail.com>;

Date:  Sun, Mar 17, 2024 05:30 AM

To:  "gmx_mmpbsa"<gmx_m...@googlegroups.com>;

Subject:  Re: NAMD+MM_GBSA/PBSA

 

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[marioe911116]

Can you point out where exactly is the issue? perhaps upload a picture of a result file where you identified the issue

[臧敏]

The questions (in picture form) are packed in my folder with the parameters [&decomp (idecomp=2, dec_verbose=3, print_res="A/1-223 B/1-57" )] were added to the origin mmpbsa.in.
In the Backbone Energy Decomposition section of the FINAL_DECOMP_MMPBSA.dat, as shown in the "Backbone_Energy_Decomposition" image, I found that the backbone energy decomposition for all C-termius of the two proteins is 0 and as is the backbone of the HSD residue.  I think this is very abnormal. Are there any files I should change, I think I'm strictly following the tutorial in the README file.

 

------------------ Original ------------------

From:  "marioe911116"<marioe...@gmail.com>;

Date:  Wed, Mar 20, 2024 02:07 AM

To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/43a011c3-4617-44c8-8b03-ae727a122fe4n%40googlegroups.com.

[marioe911116]

it seems this issue is related to some bug with the original decomposition code in sander (from Amber suite) and that's why it does not parse the BDC energy for terminals or aminoacids like HSD. I tried different methods with different topologies and always the same result. For the time being, there is nothing we can do other than report this issue to the sander developers and see what they say.

[臧敏]

Thanks a lot!

Best wishes,

Betsy

 

------------------ Original ------------------

From:  "marioe911116"<marioe...@gmail.com>;

Date:  Mon, Mar 25, 2024 05:26 AM

To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/75d4ae05-7ed1-43d2-a948-b3a6a5587d10n%40googlegroups.com.