User: ac.research

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Posts by ac.research

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Comment: C: Ligand Docking Simulation Programs
... I tried that (forum link of my question: https://www.biostars.org/p/266917/#266953). And you are right, AutoDock Vina (works nicely) is different from AutoDockTools (does no work). Unfortunately you cannot run AutoDock Vina without preparing and converting the .pdb files to .pdbqt files using AutoD ...
written 9 days ago by ac.research0
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Comment: C: Ligand Docking Simulation Programs
... yes, but AutoDockTools no longer works in new operating systems since 2014, it has not been updated since 2014 and thus is not compatible with new Python libraries (or something like that) -> it gives this error (ImportError: numpy.core.multiarray failed to import). In summary AutoDockTools does ...
written 9 days ago by ac.research0
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Comment: A: Ligand Docking Simulation Programs
... No not molecular dynamics (Gromacs), a program similar to AutoDock (which seems its autodocktools no longer installable in new operating systems since 2014) hence why I am asking for other programs. ...
written 9 days ago by ac.research0
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Ligand Docking Simulation Programs
... I have am looking to run ligand/receptor docking simulations to identify how a ligand binds to its receptor. What are the best softwares to use? ...
software question docking written 9 days ago by ac.research0
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Comment: A: AudoDockTools start software bug
... Thanks jrj.healey for your replay, I tried `python -m pip install oldnumeric` but it seems there is no oldnumeric library in pip, I get this error message: `Could not find a version that satisfies the requirement oldnumeric (from versions: ) No matching distribution found for oldnumeric` AutoDockT ...
written 12 days ago by ac.research0
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AutoDockTools start software bug
... I have Ubuntu 17.04 and i installed autodocktools as follows: `sudo apt install autodocktools` I attempt to run the program by typing autodocktools but I get the following error: `ImportError: No module named oldnumeric` I talked to some people in the irc.freenode.net #bioinformatics channel an ...
software error written 13 days ago by ac.research0 • updated 12 days ago by t_stranger20
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Comment: C: save command output to a file in pymol
... same synthax error, pointing to the same place. ...
written 7 months ago by ac.research0 • updated 7 months ago by WouterDeCoster20k
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Comment: C: save command output to a file in pymol
... Well i think we are in the right direction, but not there yet. I do get a syntax error regarding expressing the command correctly: with open('myoutputfile.txt', 'w') as output: output.write(iterate n. CA, print resi + ':' + ss)                                                                        ...
written 7 months ago by ac.research0 • updated 7 months ago by WouterDeCoster20k
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save command output to a file in pymol
... People I need your help, I have the following command: iterate n. CA, print resi + ':' + ss I use this command in pymol to print out each residue number and its corresponding secondary structure. The command prints out the result in pymol itself. My question is: **How can I save the output f ...
bioinformatics pymol python written 7 months ago by ac.research0
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Comment: C: ncbi refseq file names meaning
... Thank you very much for your answer, I had the same question. So you explained the difference between the files viral.1.protein.faa and viral.2.protein.faa (they are the viral fasta protein database divided into two files - same goes for DNA and genbank). **What is the difference between them and ...
written 12 months ago by ac.research0

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