AMBER on clustervison

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:

1. coordinate file, which contains the Cartesian coordinates of all atoms

2. topology file, which specifies the connection among the atoms and details of the interaction terms

3. 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:

1. ethane.inpcrd: http://docs.google.com/Doc?id=dfvdq4zs_104gqz2np
2. ethane.prmtop: http://docs.google.com/Doc?id=dfvdq4zs_105c99fcx
3. 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.

1. serial: (serial.sh): http://docs.google.com/Doc?id=dfvdq4zs_108drh4qw
2. 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