SamuelGong

Results 9 comments of SamuelGong

hhalignment: did not find [x] match states in sequence [i]

This also happened to one protein sequence I'm working on, while no similar problem for other sequences.

analyzing error using tutorial.tgz

Thanks for your suggestion! I configured gmx cuda version, not gmx_mpi. Would this be the reason of the error? I checked log files in md of both protein and water,...

Issues with Sidechain packing

Hi, I am also trying to do side chain packing and refinement. Can you share your full command with options? Thanks

demo_6zcy: ccd prediction (demo_6zcy.json) by helixfold3 is ok, but smiles (demo_6zcy_smiles.json) failed

Yes, ligand conformation generation from smiles failed. I tried quite a few times, with same failing message. openbabel/rdkit version like this: openbabel 3.1.1 py39h2d01fe1_9 conda-forge rdkit 2024.3.5 pypi_0 pypi rdkit-pypi...

Error when running replicadock2

I am encountered with the same error as 957_z when using mpi compiled rosetta. Confused where the number of exchange cells is set? And why error says "has to be...

`multi_pose_sampling` does not write `summary.csv` and does return per residue pLDDT scores

Yes, it works fine just printing plddt and plddt_lig, while "sample" gives huge matrix setting return_avg_stats=False.

How much time is required for making environment?

Check the closed issue "make environment fail". It works for me following the instructions.

How much time is required for making environment?

I've followed this one: https://github.com/zrqiao/NeuralPLexer/issues/1#issuecomment-1943617144 > Hi @Samuel-gwb, I have the same experience as @jianqingzheng. As per your recommendation, I read through the closed issue you are referring to. Kindly...

is there pretrained models for alphafold3?

Same question ....