System setup using Amber

  • Generate the structure of DNA using tools like NAB, CHIMERA etc.
  • Generate the ligand structure using GaussView or Avogardo2
  • Run antechamber to obtain amber suitable structure as prepi or mol2 (mol2 is a preferred format). Then parmchk2 to convert it to simulation format interaction.
antechamber -fi pdb -fo prepi -i ligand.pdb -o ligand.prepi -rn LIG -c bcc -at gaff2
parmchk2 -f prepi -i ligand.prepi -o ligand.frcmod
  • Add the dna, ligand and protein using tleap.
  • Execute a tleap file using tleap -s -f tleap.in > out.txt

Amber

  • location of leaprc files $AMBERHOME/dat/leap/cmd

Protein modelling

Homology modelling for a missing residue:

  • Easiest way to install modeller is through conda ```bash mamba install -c salilab modeller

```

  • Add the modeller license to the license as specified by the installer code.
  • Figure out the modeller executable name, which should be in the following format modVersion, for my case it is mod10.5
  • Modeller can be run manually following the documentation but Chimera already has a prebuilt function and beautiful visualizer to help us out.
  • Load the structure which needs has the missing residues, for my case I am opening 5L2I.

Special Comments

  • CYS represents normal cysteine residues, while -ve charge or the depronated state is written as CYM and cysteine with disulphide bond or other special bonds are written as CYX. [1]

References

  1. Amber tutorial A1