AMBER Archive (2006)

Subject: RE: AMBER: Potential Energy Calculation

From: Hayden Eastwood (
Date: Mon Nov 06 2006 - 06:47:00 CST

Hi Sangeeta

I don't know if this will be helpful to you, but I always get single point
energies of NMR and crystal structures by running a minimization with just 1
minimization step. The output energy is tantamount to a single point energy,
and the output structure will have an RMS deviation from the original
structure that is extremely small (in my case undetectably small (i.e.
0.0001 difference in RMS or something of that order).

Hope that helps


-----Original Message-----
From: [] On Behalf Of
Sent: 06 November 2006 12:12
Subject: AMBER: Potential Energy Calculation

Dear Amber Community,

I would like to compare the potential energy (PE) values of peptide
conformations that are generated in an MD trajectory and subsequently
energy-minimized, with the PE of the experimentally obtained (crystal or
solution) structure.
What is the recommended protocol for calculating "static" or single point
(potential) energy using AMBER (in order to obtain the PE of the
experimental structure)?

I tried this using energy minimization with parameters identical to those
used for post-MD minimization except for two changes: NTMIN changed from 1
to 2 and the number of iterations of steepest descent reduced to 10. The
initial energy, RMS and GMAX values (at NSTEP = 1) reported in the output
are high and positive. The input script I used is as follows:
  imin = 1, ntmin = 2
  maxcyc = 10,
  ntb = 0,
  igb = 1,
  cut = 12

Is it correct to consider the initial energy as the PE of the conformation?
(Note: I have used Amber 9 and the simulations have been carried out using
GBSA solvent model.)

Thanks in advance for any help,

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