User: ac.research

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Posts by ac.research

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Answer: A: How to upload fasta file to SSH Supercomputer
... There is a very simple command: scp from to Example to supercomputer: scp /path/to/your/file username@132.343.12.3:/path/to/your/destination/on/supercomputer scp /home/acresearch/desktop/uniprot90 acresearch@castor:/home/acresearch/databses Example from supercomputer: scp userna ...
written 5 weeks ago by ac.research0
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Comment: C: PSIPRED, how to install and make it work?
... It works now, I had an issue with the makeblastdb command (a typo as you said). Thank you very much. ...
written 5 weeks ago by ac.research0
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Comment: C: PSIPRED, how to install and make it work?
... I changed the commands to the following: wget ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz gunzip -v uniref90.fasta.gz makeblastdb -in uniref90.fasta -dbtype prot -input_type fasta -out uniref90.fasta And the database seems to setup ok (no errors printe ...
written 5 weeks ago by ac.research0
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Comment: C: PSIPRED, how to install and make it work?
... Thank you for your replay. I think the problem I am facing is with the database setup, these are the steps I follow to setup the UniProt90 database (slightly changed from the top and without using pfilt as you advised): wget ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90. ...
written 5 weeks ago by ac.research0
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Comment: C: PSIPRED, how to install and make it work?
... I followed these instructions, but they are 4 years old and it seems there has been major changes to the PSIPRED program as well as others. Hence the steps in that forum entry do not work anymore. ...
written 5 weeks ago by ac.research0
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PSIPRED, how to install and make it work?
... Dear All, I am trying to setup PSIPRED to run a secondary structure prediction but the README.md file is not detailed enough for a beginner like me to setup and run PSIPRED. I am trying to use it with BLAST+. I am on a Linux Ubuntu 17.04 operating system, and the following are the steps I take to ...
software error psipred blast written 5 weeks ago by ac.research0 • updated 5 weeks ago by yamule60
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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 weeks 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 weeks 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 weeks 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 weeks ago by ac.research0

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