AMBER Archive (2006)

Subject: AMBER: RE: protein simulation using AMBER

From: Ross Walker (
Date: Sat Dec 30 2006 - 00:51:09 CST

Dear Praveen,

> With a general input file shown below, total energy of
> the system (protein + water) and its components
> (electrostatic, bond, dihedral etc) are printed in the
> output file. Is there a way to output only the energy
> of the protein by just changing the input file? Does
> any one know if I need to change the source code to do
> it? Any suggestions in this regard are welcome.

No you would need to change the source code to do this. However, to do it
directly (and correctly) would be pretty hard. The problem is that when you
are using periodic boundaries with PME the electrostatic contribution is
divided up into real space and reciprocal space parts. For any given atom
some of the protein and solvent will be in the real space interaction part
while some will be in the reciprocal space. Thus extracting out just the
electrostatic energy due to protein-protein interactions would be difficult.

Note, with rigid triangulated water energy terms corresponding to angles,
dihedrals, 1-4 NB and 1-4 EEL come only from the protein. While the BOND,
EEL and VDW terms contain contributions from both the protein and the

Your best option for what you want to do, as far as I can tell, would be to
post process your mdcrd file. You could strip the solvent from your mdcrd
file and convert it to a series of amber restart files containing just the
snapshots of the protein. Then create yourself a prmtop corresponding to
just the protein. Create an input file with imin=1 and maxcyc=1. Then script
it to run through each of your protein only restart files. The step 0 in the
amber output from each run will then be the protein only energy. Note this
would take some tweaking I think to get the protein image energy included as
well but if the solvent box is large this may only be a small contribution
and the gas phase protein energies may be good enough.

Ps. it is best to post Amber related questions to the amber mailing list.
See for more info.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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