BPTI Example

Here we use AMBER to do an energy minimization of BPTI (bovine pancreatic trypsin inhibitor). This system, while rather small (536 atoms), but large enough to benefit from parallelism up to around 16 MPI tasks. Use is made of protonate and tleap to prepare the coordinates and topology for the simulation.

First execute the following script. The file 6pti.mod.pdb is an edited version of the file 6pti.pdb which is distributed by the Brookhaven Protein Data Bank The water and phosphate have been deleted and the B conformations of residues 39 and 50 have been deleted.

module load amber
protonate -d $AMBER_DAT/PROTON_INFO \
	 < 6pti.mod.pdb > 6pti.H.pdb
cat << eof > 6pti.leap
bpti = loadPdb 6pti.H.pdb
bond bpti.5.SG bpti.55.SG
bond bpti.14.SG bpti.38.SG
bond bpti.30.SG bpti.51.SG
saveAmberParm bpti prmtop prmcrd
quit
eof

tleap -f  6pti.leap

#this generates "prmcrd" and "prmtop" files

# run sander

cat << eof > min.in
#  do 200 steps of minimization:
 &cntrl
    maxcyc=200, imin=1, cut=12.0, nsnb=20, idiel=0, scee=2.0, ntpr=10,
 &end
eof

Then execute

% sander -i min.in -o 6pti.out -c prmcrd -r 6pti.xyz

from a batch script.

Help

The AMBER documentation directory $AMBERHOME/doc contains complete documentation and an introductory tutorial in Chapter 4, which is useful for getting started.

The AMBER Home Page contains an up-to-date resource for tutorials, documentation, and discussion groups.