AMBER Archive (2006)

Subject: Re: AMBER: Potential Energy Calculation

From: Mingfeng Yang (mfyang_at_gmail.com)
Date: Mon Nov 06 2006 - 15:06:18 CST

On Mon, 2006-11-06 at 07:32 -0500, Carlos Simmerling wrote:
> 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.
According to my recent experience on a small peptide. igb=7 + PARM99SB
is so far the best choice to use GB model in AMBER. At least in my case,
only this combination can give reasonable conformation for my small
peptide (10 residues). (I tried igb=5/7, parm99/99SB/03)

Mingfeng

> 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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