Evaluating different components of AMBER energy function with SANDER

Editing Evaluating different components of AMBER energy function with SANDER

After running AMBGMIN (with 'DUMPSTRUCTURES', 'SAVE 5' set in GMIN 'data' file), it is informative to examine the different components of the all-atom energy function. The AMBGMIN output contains averages over MD time steps which is not the same at the evaluation of the lowest energy state, naturally. One can use SANDER to run one step of minimisation to generate the different components of the energy function.

This is easily done. Three input files are needed prmtop, inpcrd, and mdin, along with the SANDER executable.

-> prmtop - amber topology file

-> inpcrd - amber coordinates file

-> mdin - SANDER input file

An easy way to do this is create an seperate directory via 'mkdir eval'

1. compile SANDER:

2. move files from GMIN output directory:

cp min1.rst eval/inpcrd

cp coord.prmtop eval/prmtop

cp min.in eval/mdin

3. Run SANDER:

4. output files:

Performed a sanity check between AMBGMIN and SANDER and the energies are the same.

mdinfo - Energy function output only

mdout - Total Amber output

restrt - coordinates for restarting AMBER

--mp466 17:03, 3 October 2009 (BST)