This is a brief introduction on AMBER for clustervision users (clustervision1.shef.ac.uk).
1. set up amber on clustervision
In your home directory, put the following lines into .bashrc file
export AMBERHOME=/usr/local/bin/amber
export PATH=$PATH:$AMBERHOME/exe
2. run amber (serial and parallel)
One will need at least three files for running a simulation with AMBER:
-
coordinate file, which contains the Cartesian coordinates of all atoms
-
topology file, which specifies the connection among the atoms and details of the interaction terms
-
parameter file, which tells how to run the simulation
For instance, to run a md simulation of ethane, the details of the three files can be found:
- ethane.inpcrd: http://docs.google.com/Doc?id=dfvdq4zs_104gqz2np
- ethane.prmtop: http://docs.google.com/Doc?id=dfvdq4zs_105c99fcx
- ethane.mdin: http://docs.google.com/Doc?id=dfvdq4zs_106c2nmkt
There are two scripts used to run serial and parallel amber jobs on clustervision, respectively.
- serial: (serial.sh): http://docs.google.com/Doc?id=dfvdq4zs_108drh4qw
- parallel: (parallel.sh): http://docs.google.com/Doc?id=dfvdq4zs_109zzsd5s
submit to clustervision1 by command:
qsub serial.sh or qsub parallel.sh
3. make input file (with leap)
xleap -s -f leaprc.glycam04
model=sequence {OME 4MA 4MA 0MA}
charge model
saveamberparm model admanp3.top admanp3.crd
savePDB model admanp3.pdb
model2=copy model
loadoff solvents.lib
solvatebox model TIP3PBOX 10.0
saveamberparm model admanp3water.top admanp3water.crd
savePDB model admanp3water.pdb
quit
4. work with dlpoly
antechamber -i cn.pdb -fi pdb -o cn.mol2 -fo mol2 -c bcc
parmchk -i cn.mol2 -f mol2 -o frcmod
with tleap (or xleap) program:
tleap -s -f leaprc.gaff
mods=loadamberparams frcmod
model=loadmol2 cn.mol2
saveamberparm model cn.top cn.crd
quit
after that, run
amb2dl.pl cn
you will get the CONFIG and FIELD files (cn.cfg and cn.fld) for DLPOLY.
Want more?
http://amber.scripps.edu/tutorials/
http://amber.scripps.edu/doc9/amber9.pdf
