AMBER Archive (2006)

Subject: AMBER: Potential Energy Calculation

From: sangeeta (sangeeta_at_bioinfo.ernet.in)
Date: Mon Nov 06 2006 - 06:11:30 CST

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:
 &cntrl
  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,
Sangeeta 

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