The 13th faculty

This one is an unexpected gift from a bid.

This is a pure mechanical camera, with maximum 1/500 shutter speed. I have loaded a roll of kodak iso 200 film. The batteries specified in the manual (Mallory D386) are difficult to find. Fortunately, LR43 and SR43SW can be used instead. So far I have roughly 20 shots. Will post some photos after the film developed.

$ pdb2gmx -ignh -ff G43a2 -f Chk1.pdb -o Chk1.gro -p Chk1.top -water spce
$ cat 43A.gro >> Chk1.gro
$ vi Chk1.gro           # modify atom numbers
$ vi Chk1.top           # add drug top file
$ editconf -bt cubic -f Chk1.gro -o Chk1.gro -d 0.9
$ genbox -cp Chk1.gro -cs spc216.gro -o Chk1_b4ion.gro -p Chk1.top
$ grompp -f em.mdp -c Chk1_b4ion.gro -p Chk1.top -o Chk1_b4ion.tpr  # note charges
$ genion -s Chk1_b4ion.tpr -o Chk1_b4em.gro -nname NA+ -nn 7 -g Chk1_ion.log
$ vi Chk1.top          # add NA+ and substract SOL

# run energy minimization
$ grompp -f em.mdp -c Chk1_b4em.gro -p Chk1.top -o em.tpr
$ mdrun -v -deffnm em

# run position restraint dynamics
$ grompp -f pr.mdp -c em.gro -p Chk1.top -o pr.tpr
$ mdrun -v -deffnm pr

# run molecular dynamics
$ grompp -f md.mdp -c pr.gro -p Chk1.top -o md.tpr
$ mdrun -v -deffnm md

After the midterm, I got some compound structures to eveluate. I was asked to consider explicit solvent, which is not possible with DOCK. Therefore I chose GROMACS for dynamics between these compounds and the protein.

There is an excellent GROMACS tutorial on drug/protein complex by John E. Kerrigan of University of Medicine and Dentistry of NJ. However, this tutorial was written for GROMACS 3.3.1, and the current GROMACS version is 4.04. Some small modifications are necessary.

1. Use PRODRG beta server insetad of the old version. The beta version use newer force fields (GROMOS96.1) and with more outputs. Use DRGGMX.ITP and DRGAPH.GRO.

2. When converting protein structure with pdb2gmx, use GROMOS96 force field (GROMOS96 G43a2) instead of gmx (GROMOS87).

3. When neutralizing charges, use CL- and NA+.

There might be other changes, but they could wait till tomorrow...