Yasser Almeida
Yasser Almeida
Hello, I am modeling a multimer composed of a monomer that binds to a homodimer. The monomer in solution adopts a conformation but when bound to the dimer, it suffers...
Hello, I ran AlphaFold-Multimers Colab ([https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb](url)) but the results cannot be downloaded. Below is the error: ``` NotImplementedError Traceback (most recent call last) [](https://localhost:8080/#) in () 210 211 # ---...
Hello, Is it possible to use the MSAs generated by AlphaFold, converted as .a3m format, for multi-chain predictions? Regards
Hello, When I run `mdbenchmark generate -n benchmark_G4x --module gromacs/2020.1 --max-nodes 2` I get: ``` Traceback (most recent call last): File "/home/adi865j/.local/bin/mdbenchmark", line 5, in from mdbenchmark import cli File...
Hello, I've seen in release tag v1.5.3 ([https://github.com/ccsb-scripps/AutoDock-GPU/releases/tag/v1.5.3](url)) the Boron atom type was added. However, I cannot find those parameters in the source code. I would appreciate it if you...
Hello, I saw that AutoDock-GPU added the parameters for Boron ([https://github.com/ccsb-scripps/AutoDock-GPU/releases/tag/v1.5.3](url)) Is it possible to add them to AutoDock-Vina? After my post in AutoDock-GPU ([https://github.com/ccsb-scripps/AutoDock-GPU/issues/217](url)) I was directed to the...
Hello, I installed the package and when I tried to load a topology/trajectory (both psf/dcd or tpr/xtc) I got this error with the BCL library: ``` BCL Error: -1 |...
Hello, I am trying to run RFDiffusion in my HPC with Singularity (I don't have Docker). I generated the SIF image with `singularity build rfdiffusion.sif docker://stephenturner/rfdiffusion`. Could you provide instructions...
Hello, I am playing with the `hadress_water/water.py` to learn AdresS. My end problem is based in a similar system of the example, but with a sphere configuration of the atomistic...
Hello, I am using the [https://www.biotite-python.org/latest/examples/gallery/structure/modeling/trajectory_sse.html]() code to generate the secondary structure plot but I am getting the following error: ``` Traceback (most recent call last): File "/media/Data2/CIM/IL2/2023/IL2wt/analysis/./trajectory_sse.py", line 48,...