1. Amber 10 Tutorial Minimization in Sander

2. Minimization It is important to do a quick read of pg. 21 and the start of pg 22 of Amber10 Manual.pdf. These 2 pages show the syntax of how to run the sander command function. All page numbers here will refer to the “Amber10 Manual.pdf”

3. minimization.sh The code below is the code to run a minimization in sander. It will be described in detail in the next few slides. #Running minimization for lys w/ H20 cat min.in #5000 steps of minimization &cntrl maxcyc=5000,imin=1,ntx=1,ntwx=0,ntwv=0,ntwe=1, ncyc=20,ntmin=1,drms=1.0E-4,ntb=1,cut=12.0, igb=0, / EOF echo 'begin bnr minimization' >> timer.dat date >> timer.dat bnra=/home/saguaro/Quickgo/amber10tutorial sander -i min.in -o min.out -p $bnra/bnrwh2o.top -c $bnra/bnrwh2o.crd -r min.rst -e min.ene date >> timer.dat echo 'end bnr minimization' >> timer.da t

4. Min.in maxcyc = 5000pg 27 – maximum number of cycles the minimizations will run before it stops – like NSTEP in saguaro imin = 1pg 23 – 1 means do minimization and no molecular dynamics – same as imin in saguaro except an analysis option, imin = 5 ntx = 1pg 24 – reads in formatted (i.e. not binary) coordinates without velocites – similar to iCRD in saguaro, but NOT the same. ntwx,ntwv,ntwe = #pg 25,26 – these denote the number (#) of steps between writing the positions (x), velocities (v), or energies (e) of the run. – minimization doesn’t write any of these out.

5. Min.in ntmin = 1pg 27 – applies the stepest descent algorithm to the minimization run for ncyc then switches to the conjugate gradient. ncyc = 20pg 27 – 20 steps before the run switches to conjugate gradient. drms = 1.0E-4pg 27 – the run will stop when the root-mean-square of the coordinates of the gradient is less than this value. Units are in kcal/(mol-angstrom) ntb = 1pg 35 – this is periodic boundary conditions (constant volume) – this is the same as iPBC in saguaro cut = 12.0pg 35 – non-bonded cutoff in angstroms. I should have used 8 here because this is explicit water. igb = 0pg 36 & 54 – 0 turns off generalized born. Unlike saguaro there are a lot of gb types to choose from

6. Minimization An example run of this can be found on saguaro@dnaseq in the directory ~/Quickgo/amber10tutorial/bnrMD/minimize/