AMBER Archive (2006)

Subject: Re: AMBER: Potential Energy Calculation

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon Nov 06 2006 - 06:32:35 CST

I strongly recommend against using igb=1 for peptide simulations
unless you are very familiar with its weaknesses. Along with articles
by other labs, we have published two articles this year in J. Chem.
Theory & Comput
showing that igb=1 has strong biases for both salt bridges and
specific protein backbone conformations. igb=5 is much better in
both respects.
carlos

Investigation of Salt Bridge Stability in a Generalized Born Solvent Model
Geney, R.; Layten, M.; Gomperts, R.; Hornak, V.; Simmerling, C.
J. Chem. Theory and Comput.; (Article); 2006; 2(1); 115-127.

Improved Efficiency of Replica Exchange Simulations through Use of a
Hybrid Explicit/Implicit Solvation Model
Okur, A.; Wickstrom, L.; Layten, M.; Geney, R.; Song, K.; Hornak, V.;
Simmerling, C.
J. Chem. Theory and Comput.; (Article); 2006; 2(2); 420-433.

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_stonybrook.edu
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================

sangeeta wrote:

>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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