AMBERTOOLS21

How to use AMBERTOOLS21

Description

Amber is a suite of biomolecular simulation programs. It began in the late 1970’s, and is maintained by an active development community; see our history page and our contributors page for more information.

The term “Amber” refers to two things. First, it is a set of molecular mechanical force fields for the simulation of biomolecules (these force fields are in the public domain, and are used in a variety of simulation programs). Second, it is a package of molecular simulation programs which includes source code and demos.

Amber is distributed in two parts: AmberTools21 and Amber20. You can use AmberTools21 without Amber20, but not vice versa.

AmberTools21 are compiled in parallel with OpenMPI. There are currently three ways to use it.

The first way is to run the command Launch_sander_s1 for the <first step>, this launcher calls "sander.MPI" and you will have to enter the following parameters:

Launch_sander_s1 [nprcos] [input_file] [output_file] [prmtop_file] [inpcrd_file] [rst_file]
Second way is to run the command Launch_sander_s2 (to relaunch the calculation) for the <second step>, this launcher calls "sander.MPI" and you will have to enter the following parameters:
 
Launch_sander_s2 [nprcos] [input_file] [output_file] [prmtop_file] [inpcrd_file] [rst_file] [crd_file]
Third way, AmberTools21/Gaussian 16. If you need to use Amber with Gaussian you should run Launch_Ag16 
launcher.

Launch_Ag16 [nprocs][input_file][output_file][prmtop_file][inpcrd_file][rst_file]

(Remember that you also need a ".tpl" file with the Gaussian input data)


Example An input file for QM or QM/MM MD with Gaussian using the BP86 functional and the 6-31G**
basis set and running in parallel on 8 threads (using 1 GB of memory) therefore would have to contain

&gau
method = 'BP86',
basis = '6-31G**',
num_threads = 8,
mem='1GB',
/


Template input file The template file for Gaussian should be named gau_job.tpl and should only contain the
route section of a Gaussian input file. The route section defines the method to be used and SCF convergence
criteria. Charge and spin multiplicity are specified via the &qmmm namelist. For example for a B3LYP
calculation with 6-31G* basis set, the route section would be:
#P B3LYP/6-31G* SCF=(Conver=8)

Do not include any information about coordinates or point charge treatment since this will all be handled by sander.
Also, do not include any Link 0 Commands (line starting with %) since these are handled by sander. If you want
to run Gaussian in parallel, specify the number of processors via the num_threads variable in the &gau namelist