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Description Content
module load chem/amber
License Amber is not free. Academic/non-profit/government: $500.

Amber-Tools are free.


D.A. Case, J.T. Berryman, R.M. Betz, D.S. Cerutti, T.E. Cheatham, III,
T.A. Darden, R.E. Duke, T.J. Giese, H. Gohlke, A.W. Goetz, N. Homeyer,
S. Izadi, P. Janowski, J. Kaus, A. Kovalenko, T.S. Lee, S. LeGrand, P. Li,
T. Luchko, R. Luo, B. Madej, K.M. Merz, G. Monard, P. Needham,
H. Nguyen, H.T. Nguyen, I. Omelyan, A. Onufriev, D.R. Roe, A. Roitberg,
R. Salomon-Ferrer, C.L. Simmerling, W. Smith, J. Swails, R.C. Walker,
J. Wang, R.M. Wolf, X. Wu, D.M. York and P.A. Kollman (2015),
AMBER 2015, University of California, San Francisco.

Links Amber Homepage | Amber Wiki | Manual Page
Graphical Interface No
Included modules mpi/openmpi numlib/mkl compiler/intel
Additive software Amber-Tools

1 Description

Amber refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs.
This module provides the molecular dynamics package AMBER via command 'sander' or 'pmemd' ... see also.

AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. The sander program is now a part of AmberTools.

For more information on features please visit The Amber Homepage.

2 Versions and Availability

A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the

Cluster Information System CIS

On the command line interface of any bwHPC cluster you'll get a list of available versions by using the command
'module avail chem/amber'.

$ module avail chem/amber
-------------------- /opt/bwhpc/common/modulefiles ---------------------

3 License

3.1 Amber License and Order

Click here for the Amber License Agreement. Print this form, fill it out, sign and return (with your payment) to the address given at the bottom of the license agreement.
Amber is now distributed electronically; once your order is processed, you will receive download information via email. PDF versions of the Reference Manual are included in the download.
Fees: Academic/non-profit/government: $500. Porting and demonstration licenses are available, as are licenses for computing centers; see the License Agreement for details.
See also: Ordering Amber
You will also need to download and install AmberTools.

3.2 Amber-Tools

The Amber-Tools programs here are mostly released under the GNU General Public License (GPL). A few components are included that are in the public domain or which have other, open-source, licenses.
See also: Amber-Tools.

4 Usage

4.1 Loading the module

You can load the default version of Amber (e.g. version 12) with the command
'module avail chem/amber'.

$ module avail chem/amber
-------------------- /opt/bwhpc/common/modulefiles ---------------------
$ module load chem/amber
Please do not use this module if you do not own a valid AMBER group license.
Please cite AMBER in your publications according to AMBER documentation.
Please read 'module help chem/amber/12' before using AMBER.

The module will try to load modules it needs to function (e.g. compiler, mpi, numlibs).

If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for Amber.
If you wish to load a specific (older) version (if available), you can do so using e.g. 'module load chem/amber/version' to load the version you desires.

$ module avail chem/amber
------------------------ /opt/bwhpc/common/modulefiles -------------------------
$ module load chem/amber/12
Please do not use this module if you do not own a valid AMBER group license.
Please cite AMBER in your publications according to AMBER documentation.
Please read 'module help chem/amber/12' before using AMBER.

4.2 Program Binaries

You can find the Amber binaries in the $AMBER_BIN_DIR-folder of the Amber system. $AMBER_BIN_DIR points to $AMBER_HOME_DIR/bin.
After loading the Amber module ('module load chem/amber') this path is also set to the local $PATH- and the $AMBER_BIN_DIR environments.

$ module list
Currently Loaded Modulefiles:
  1) compiler/intel/13.1            3) numlib/mkl/11.0.5
  2) mpi/openmpi/1.6.5-intel-13.1   4) chem/amber/12
acdoctor*             matgen*                 process_minout.perl*
addles*               matmerge*               PropPDB*
add_pdb*              matmul*                 protonator*
AddToBox*             MCPB*                   ptraj*
add_xray*             mdgx*                   pymdpbsa@
am1bcc*               mdnab*                  pytleap@
ambmask*    *        rdparm*
ambpdb*               minab*                  reduce*
antechamber*          mmE*                    residuegen**       MMPBSA_mods/            resp*
atomtype*             mm_pbsa_nabnmode*       respgen*
bondtype*   *             rism1d*
calcpka*    *              rism3d.snglpnt*
capActiveSite*        mmpbsa_py_energy*       sander*
chamber*    *          sander.LES*
charmmgen*            mmpbsa_py_nabnmode*     sander.LES.MPI*
charmmlipid2amber.x**  sander.MPI*
ChBox*                molsurf*                senergy*
CheckMD*              mpi4py/                 sequenceAligner*
chemistry/            mpinab*       **          mpinab2c*     *
cpinutils/            MTKppConstants**
cpptraj*              nab*                    sqm*
database*             nab2c*                  stats*
elsize*               ncdump*                 stdLib2Sdf*
espgen*               ncgen*                  superimposer*
fantasian*            new2oldparm*            sviol*
ffgbsa*               nmode*                  sviol2*
fftw-wisdom*          paramfit*               teLeap*
fftw-wisdom-to-conf*  parmcal*                tleap*
frcmod2xml*           parmchk*                top2mol2*
func*       *              transform*
hcp_getpdb*           ParmedTools/            translate*
hybrid*               pbsa*                   tss_init*
lmodprmtop*           pdbSearcher*            tss_main*
makeANG_RST*          pmemd*                  tss_next*
makeCHIR_RST*         pmemd.amoeba*           ucpp*
make_crd_hg*          pmemd.amoeba.MPI*       UnitCell*
makeDIP_RST.dna*      pmemd.MPI*              xaLeap*
makeDIP_RST.protein*  prep2xml*               xleap*
makeDIST_RST*         prepgen*      *
matextract*           process_mdout.perl*     yacc*

A '/' at the end of a file name indicates a directory/folder. '*' is an executable. The Amber-Tools files are linked (ln -s) to the $AMBER_BIN_DIR, too.
Use programs with the suffix .MPI for MPI releated binaries.

4.3 Disk Usage

Scratch files are written to the current directory by default. Please change to a local directory or to your local workspace (preferred) before starting your calculations.
'amber_repo' is an example name of a repository you created by using the command 'ws_allocate'.

$ cd $(ws_find amber_repo)
['your-id'-amber_repo-0]$ pwd

5 Examples

5.1 bwHPC examples

You can copy a simple interactive example to your workspace and run it, using msub

$ cd $(ws_find amber_repo)
$ cp $AMBER_EXA_DIR/* .
$ cp bwunicluster-amber-example.moab myamberjob.moab 
§ vi myamberjob.moab         # do your own modifications
$ msub myamberjob.moab       # start job submission

5.2 Excerpt from bwhpc Moab submit-script

echo " "
echo "### Copying input test files for job (if required):"
echo " "
cp ${AMBER_HOME}/test/tip4p/* .
cat > mdin <<EXAMPLE
 equilibration, polarizable solute
  irest  = 1, ntx    = 7,
  ntb    = 2, ntp    = 1, taup=0.5,
  cut    = 8.0,
  ntf=2, ntc=2, tol=0.000001,
  nstlim=10, ntpr=1,
  ntt=1, temp0=300., tautp=0.5,
  jfastw=1, watnam='TP4'
echo " "
echo "### Calling amber command ..."
echo " " 
# use suffix '*MPI' for MPI binaries
time mpirun -v -np ${MOAB_PROCCOUNT} sander.MPI -O -i mdin -c eq12.x -o mdout

6 Amber-Specific Environments

To see a list of all Amber environments set by the 'module load'-command use 'env | grep AMBER'.
Or use the command 'module display chem/amber'.
Example (e.g. Amber 12)

$ env | grep AMBER

7 Version-Specific Information

For a more detailed information specific to a specific Amber version, see the information available via the module system with the command 'module help chem/amber/version'.
For a small abstract what Amber is about use the command 'module whatis chem/amber/version'.
Example (Amber 12)

$ module whatis chem/amber/12
chem/amber/12        : AMBER (and Amber-Tools) molecular dynamics version 12 (command 'sander' or 'pmemd')
$ module help chem/amber/12
----------- Module Specific Help for 'chem/amber/12' --------------
This module provides the molecular dynamics package AMBER version 12
via command 'sander' or 'pmemd' (see also
Amber-Tools 12 are included, too.
*  Example data and a Moabexample script can be found here:
This version is compiled with openmpi, mkl using the intel compiler.

8 Amber-related links