How to prepare ligand libraries for docking with Vina

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  • เผยแพร่เมื่อ 24 ธ.ค. 2024

ความคิดเห็น • 9

  • @Anu-mp9en
    @Anu-mp9en ปีที่แล้ว

    Sir, Can we use the pdbqt files for pyrx software also?

    • @al1r3z49
      @al1r3z49  ปีที่แล้ว +1

      Sorry for my late answer. Yes you can, I think it has also tools for analyzing docking interactions too.

  • @ManishKumar-by5jw
    @ManishKumar-by5jw 3 ปีที่แล้ว

    Can you provide the ligand files you used, or can you suggest some of website which provides the ligand libraries for free specially for natural compounds..

    • @al1r3z49
      @al1r3z49  3 ปีที่แล้ว +2

      You can use Drugbank, LifeChemicals, ASINEX, and ZINC natural product databases. These are very helpful.

  • @archnayadav727
    @archnayadav727 2 ปีที่แล้ว

    I have optimised my ligand with Marvin sketch and added gasteier charge, even there comes an error that there is no atomic partial charge on ligand,can u plz give me any solution

    • @al1r3z49
      @al1r3z49  2 ปีที่แล้ว

      @aarchna_yadav I've saw similar errors in PDB files. I used spdbv software back then. It has an option; select all the atoms then Tools --> Fix Selected Side Chains --> Quick and Dirty. After that save the current layer into a new file. I think it might help.

  • @ManishKumar-by5jw
    @ManishKumar-by5jw 3 ปีที่แล้ว +1

    Please provide the command code.. Thanks in advance..

    • @al1r3z49
      @al1r3z49  3 ปีที่แล้ว +2

      After copying babel.exe, use this: babel.exe *.sdf -opdbt -m
      *.sdf implicates all files containing .sdf string. -opdbqt defines the format of the outputs . And -m is for spiting.

    • @ManishKumar-by5jw
      @ManishKumar-by5jw 3 ปีที่แล้ว

      @@al1r3z49 thanks a lot..