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Amber 10 Tutorial

Amber 10 Tutorial. Minimization in Sander. 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”.

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Amber 10 Tutorial

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  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 << EOF > 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 -imin.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.dat

  4. Min.in • maxcyc = 5000 pg 27 • maximum number of cycles the minimizations will run before it stops • like NSTEP in saguaro • imin = 1 pg 23 • 1 means do minimization and no molecular dynamics • same as imin in saguaro except an analysis option, imin = 5 • ntx = 1 pg 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 = 1 pg 27 • applies the stepest descent algorithm to the minimization run for ncyc then switches to the conjugate gradient. • ncyc = 20 pg 27 • 20 steps before the run switches to conjugate gradient. • drms = 1.0E-4 pg 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 = 1 pg 35 • this is periodic boundary conditions (constant volume) • this is the same as iPBC in saguaro • cut = 12.0 pg 35 • non-bonded cutoff in angstroms. I should have used 8 here because this is explicit water. • igb = 0 pg 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/

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