Page UDPGlcNAc

• PDB Entry 1VGV contains a structure of UDP-GlcNAc-Epimerase with bound UDP-GalNAc (it rather looks like UDP-ManNAc?!)
• given the coordinates of the bound UDP-GalNAc structure the simulation data of UDP-GlcNAc was analysed again
• peptide trajectory c16.trr almost matched the bound UDP-GalNAc conformation
• screening of the water data is currently carried out (calculation of dihedral RMSD)

Gromacs Commands

• Add Box Coordinates to Coordinate File

  editconf_d -bt cubic -c -f 1.gro -o 1_box.gro -d 1.2

• Solvate Created Box using AMBER TIP3 Water

  genbox_d -cp 1_box.gro -cs ffamber_tip3p.gro -o 1_box_em.gro -p UDPGlcNAc_new.top

• Prepare Generic Input File for Energy Minimization (Water only)

  grompp_d -f ../em.mdp -c 1_box_em.gro -p UDPGlcNAc_new.top -o 1_em.tpr 

• Add Ion

  genion_d -s 1_em.tpr -o 1_ion.gro -pname Mg -pq 2 -np 1 -g log

• Reposition Ion

   ../scripts/ionPlacement.pl 1_ion.gro 35 > 1_ion_repl.gro

• Prepare Generic Input File for Energy Minimization (Ion Added)

  grompp_d -f ../em_ion.mdp -c 1_ion.gro -p UDPGlcNAc_new_ion.top-o 1_ion.tpr

• Run Energy Minimization for Ion File

  mdrun_d -s 1_ion.tpr -o 1_ion.trr -c 1_ion_min.gro  

• Prepare Generic Input File For Production Run Ion

  grompp_d -f ../run.mdp -c 1_ion_min.gro -p UDPGlcNAc_new_ion.top -o ion_run.tpr

• Start Production Simulation of Ion File (including equilibration phase)

  mdrun_d -v -s ion_run.tpr -o 1_ion_run.trr -c run.gro

• Start Production Simulation of Water File (including equilibration phase)

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