Samuel Genheden, 2012
Create a folder for each ligand, e.g., L02, L03. In each of these folder create two additional folders: Params and Sim_gb
prmtop and prmcrd filesParams
Copy the following files from /away/bio/Data/Amber/Gal3
l02_ff94.in
gal-l02_nowat.pdb
Change l02 to the ligand you are working with.
Enter the command
tleap
that starts the program leap, which will be used to create the parameter/topology file (prmtop) and the coordinate file (prmcrd) that will be used to run the simulation.
In leap, enter the following commands:
source leaprc.ff99SB
loadamberparams gaff.dat
loadamberprep l02_ff94.in
x=loadpdb gal-l02_nowat.pdb
set default pbradii bondi
saveamberparm x prmtop prmcrd
quit
These commands can also be put in a file and executed in the following way: tleap -f leapcom where leapcom is the name of the file with all commands. Change l02 to the ligand you are working with. Change bondi to mbondi2 if you are gonna simulate with igb=2.
Copy the prmtop and prmcrd files to ../Sim_gb and goto that folder.
/away/bio/Sim_scripts/
equil_platon_gb.bash
prod_platon_gb.bash prmtop and prmcrd to a corresponding folder on Platon (unless you are doing all this on Platon).
When you are on Platon, goto the Sim_gb folder and run
bash equil_platon_gb.bash prmtop prmcrd 48 l02 7
and it will run a ~1 ns equilibration simulation. The number 48 is for now an educated guess for how long time it will take. It might be much faster. l02 is just a string (it could be any string) that is appended to the queue-scripts. 7 is the GB-model.
When it is finished, run
bash prod_platon_gb.bash prmtop prmcrd 24 l02 7
that will start and put 40 independent simulations in the queue
Note that there are two files
equil_abisko_gb.bash
prod_abisko_gb.bash
that can be used to execute the simulations on Abisko.
and
equil_alarik_gb.bash
prod_alarik_gb.bash
that can be used to execute the simulations on Alarik.