srilekha1993

Hi All, After getting the output signal from cppflow::encode_wav(), what function of cppflow we will use to write it in the ".wav" format. I want to get a .wav file...

Missing centre grid co-ordinates and size_x, size_y and size_z value in 140 complex dataset to apply for Autodock Vina

5

As vina need the center grid co-ordinates and size_x,size_y,size_z values but the dataset only contains grid maps. Is there any way to evaluate these co-ordinates?

local search method sw used in autodock gpu is similar to psw for autodock cpu?

2

As our aim is to compare the energy values of autodock cpu and gpu but autodock gpu is not supported by psw algorithm and autodock cpu is not sw algorithm....

Energy interpretation of Autodock cpu output in dlg format

1

[1jla_psw.txt](https://github.com/ccsb-scripps/AutoDock-GPU/files/15157453/1jla_psw.txt) The above file is the output of autodock cpu. Can anyone help me out what is the final energy value after docking?

output2, state2 = self.lstm2(tf.concat([padding, output1], 1), state2) in model.py

Vina runtime error: The ligand is outside the grid box

1

I have tried with 5 lignads(such as 5wl0,1jla,1aet,5tim,4fev) for Vina GPU with the center values and box volume(x,y,x) which worked fine while in Autodock Vina CPU(for 1.2.5) with corrosponding value...

GPU memory is used while running inference.py changing the device to cpu

1

Hi, I observed while running the command [ time python -m inference --config default_inference_args.yaml --protein_ligand_csv data/test_1.csv --out_dir results_L_cpu/user_predictions_small] the GPU memory is used while the device is changed to 'cpu'...

Hi, After running esm_embedding_preparation.py getting the following output in fasta file ^C}q^@(X^N^@^@^@4d3i_1_chain_0q^AXk^A^@^@MEEKEILWNEAKAFIAACYQELGKAAEVKDRLADIKSEIDLTGSYVHTKEELEHGAKMAWRNSNRCIGRLFWNSLNVIDRRDVRTKEEVRDALFHHIETATNNGKIRPTITIFPPEEKGEKQVEIWNHQLIRYAGYESDGERIGDPASCSLTAACEELGWRGERTDFDLLPLIFRMKGDEQPVWYELPRSLVIEVPITHPDIEAFSDLELKWYGVPIISDMKLEVGGIHYNAAPFNGWYMGTEIGARNLADEKRYDKLKKVASVIGIAADYNTDLWKDQALVELNKAVLHSYKKQGVSIVDHHTAASQFKRFEEQAEEAGRKLTGDWTWLIPPISPAATHIFHRSYDNSIVKPNYFYQDKPY Which contains some invalid characters which are not processed by scripts/extract.py for generating the embedding using esm ....

ValueError: No edges and no nodes

3

Hi @jsilter, while running inference.py for pdbbind dataset on 363 complexes mentioned in testset_csv.csv sometimes throwing the below error 48it [49:44, 25.37s/it]--- Logging error --- Traceback (most recent call last):...

Hi, As I am trying to run the code on pvcq, getting the error shown below are related to logger where my environment has torch which is intel compatible. Can...