AMBER Archive (2003)

Subject: Re: HBOND energies in sander

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Mon May 26 2003 - 12:24:01 CDT

Francisco Blanco wrote:
>
> Hi:
>
> I am running a protein energy minimiation with sanser using nmr
> restraints. This is my input file:
>
> &cntrl
> imin=1, cut=99.0, ntpr=20, dielc=1, nmropt=1, maxcyc=5000,
> ncyc=2000, ntmin=1, nsnb=20, scee=1.2, scnb=2, ntb=0,
> ipnlty=1, pencut=0.1
> &end
> &ewald
> eedmeth=5
> &end
> &wt type='END' &end
>
> An this is one of the energy reports:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 2.0204E+03 7.7222E+01 3.4922E+03 O 1359
>
> BOND = 1.2018 ANGLE = 27.1848 DIHED = 941.0910
> VDWAALS = 638.7122 EEL = -1804.2456 HBOND = 0.0000
> 1-4 VDW = 550.1841 1-4 EEL = 1418.7753 RESTRAINT = 247.4923
> EAMBER = 1772.9037
>
> Could you explain me why is HBOND equal to zero? (It is at every step).

The HBOND term refers to a Lennard-Jones 10-12 potential, which has been
used in the Weiner et al. force fields to describe non-bonded
interactions between hydrogen bond pairs. Starting with the Cornell et
al. force field (parm94), this term is omitted now, hence its value is
set to zero.

Best regards

Holger
 
> Thanks
>
> --
> Francisco Blanco
> NMR group, Structural and Computational Biology Programme
> Centro Nacional de Investigaciones Oncológicas
> Melchor Fernández Almagro 3, 28029 Madrid, Spain
> Phone: 34 91 2246983 Fax: 34 91 2246976 www.cnio.es 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++