install dependencies can't work

[puguh173224]

Hi sir, Your "make it rain" is great. The last time I tried amber and protein-ligand simulation is successful. but after that, I try again and encounter an error in the install dependencies. how to fix this problem? Thank You

[pablo-arantes]

Hi @puguh173224,

Google Colab updated to python 3.10. Now, it's having problem with OpenMM. I'm trying to fix, I will let you know when it's done.

Thank you.

[pablo-arantes]

Hi @puguh173224,

Everything is working fine now.

Thank you.

Best,

Pablo

[puguh173224]

Hi Sir, thank you for your answer. however I try to running again and it is still can not work at Parameters to generate the Amber topology How to fixed this problem? Cause I have try to read the variable data inside the looping, but still cannot read it. Thank You

On Sat, Apr 29, 2023 at 10:02 AM Pablo Ricardo Arantes < @.***> wrote:

Hi @puguh173224 https://github.com/puguh173224,

Everything is working fine now.

Thank you.

Best,

Pablo

— Reply to this email directly, view it on GitHub https://github.com/pablo-arantes/making-it-rain/issues/68#issuecomment-1528558749, or unsubscribe https://github.com/notifications/unsubscribe-auth/A7PULVO6YMZBXS3YF5TJFVDXDSADPANCNFSM6AAAAAAXPH6CVE . You are receiving this because you were mentioned.Message ID: @.***>

-- Puguh Novi Arsito, M.Sc.,Apt Dosen dan Peneliti Departemen Farmakologi dan Farmasi Klinik Prodi Farmasi Fakultas Kedokteran dan Ilmu Kesehatan Universitas Muhammadiyah Yogyakarta Jl Lingkar Selatan, Tamantirto, Kasihan, Bantul Yogyakarta 55183

[harrynov22]

I have the same problem

[pablo-arantes]

Can you please provide more information regarding the issue? And I'm a little bit confuse here, which notebook are you using? The Amber notebook or the Protein-ligand notebook?

[puguh173224]

I use amber notebook

[pablo-arantes]

Ok! Thank you for the information. This error is because tleap is not able to create your topology. Are you using your own PDB file? If yes, I suggest checking your input PDB file. Remember, the Amber notebook works only for protein, nucleic acids and glycans systems, if you have different molecule tleap will not be able to create your topology. I've tested here for the PDB ID 1AKI and everything went fine.

[puguh173224]

Yes, it was also OK when I tested for PDB ID 1 AKI. But when I use my own system PDB protein with code 5OQV, it can not create the topology. last month, before the system updated, everything worked OK. thank you.

[pablo-arantes]

Hi,

Thank you for letting me know. I've fixed the code, I've tried with your PDB ID (5OQV) and everything worked fine. Please, open the notebook again and try.

Best,

Pablo