Amber: How to set-up calculations. Preliminary Remarks. Amber is a very sophisticated piece of scientific software and as such requires some amount of time to learn it.
A person spent many days trying to minimize a structure using Gaussian…
It was no success…
One quick look immediately discovered a problem
A person spent many days running Molecular Dynamics using Amber…
He was experiencing crashes of Amber during his runs …
Visual inspection of his molecular structures showed that initial structures had had not well prepared.
Oxygen atom is missing
Incomplete valencies on atoms…
Hydrogen atom is missing
The structure also had a steric clash between two amino acid residues which could lead to a program overflow error
It is a Java program, i.e. it is cross-platform
We plan to add support for all Amber and Gaussian input and output files
Additional tutorial examples are available at http://amber.scripps.edu.
xleap -s -f <filename>
sander [-help] [-O] [-A] -i mdin -o mdout
-p prmtop -c inpcrd -r restrt -ref refc
-x mdcrd -y inptraj -v mdvel -e mden
-inf mdinfo -radii radii -cpin cpin
-cpout cpout -cprestrt cprestrt -evbin evbin
sander –O -i mdin -o mdout -p prmtop -c inpcrd
Control data for the minimization/MD run
Molecular topology, force field, periodic box type, atom and residue names
Initial coordinates and (optionally) velocities and periodic box size
Each of the variables listed below is input in a namelist statement with the namelist identifier &cntrl.
End of namelist&cntrl
Variables that are not given in the namelist input retain their default values.
Option description panel
A Java program has been written to facilitate preparation of input job control files for Sander-8 (support for Sander-9 will be added soon).
It uses intuitive controls to setup job control variables for Sander run. In many cases instead of variable\'s name it uses variable\'s description. For example, for variable NSTLIM it uses "Number of MD Steps (nstlim)".
Closely related options are grouped on separated panels which can be activated using tabs.
Options can be setup using either text fields or combo boxes.
Advanced users might want to edit program options using the built-in text editor, with the program allowing easy switching between GUI and text editing