AMBER Archive (2005)

Subject: Re: AMBER: strange VDWAALS and EEL energies calculated by pbsa

From: Ray Luo (rluo_at_uci.edu)
Date: Thu Apr 21 2005 - 07:18:17 CDT

Fabien,

The pbsa code was designed to behave this way in amber8. In amber9, all
nonbonded terms will be computed. If you don't mind reinstall your pbsa
src and test cases, I'm happy to email you the updated package. We've
checked to make sure that pbsa energies are consistent with sander
energies under identical conditions.

All the best,
Ray

Fabien Cailliez wrote:

> Dear all,
>
> I have seen strange behavior in pbsa results.
> The VDWAALS energy is always set to 0 and the EEL energy is equal to
> the ERF energy.
> I did not manage to track the problem into the code. Has anyone ever
> noticed this problem ?
>
> Thanks in advance,
> Fabien
>
> Here are the input file and the results :
>
> File generated by mm_pbsa.pl. Using PB
> &cntrl
> ntf = 1, ntb = 0,
> igb = 10, dielc = 1.0,
> cut = 99999.0, nsnb = 99999,
> scnb = 2.0, scee = 1.2,
> imin = 1, maxcyc = 0, ntmin = 2,
> &end
> &pb
> epsin = 1.0, epsout = 78.5,
> istrng = 0.15, radiopt = 0,
> sprob = 1.4, space = 0.5,
> maxitn = 500
> npbverb= 1
> &end
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 8.3130E+03 1.8081E+01 1.0436E+02 C 2133
>
> BOND = 605.6470 ANGLE = 1658.2508 DIHED =
> 2069.9663
> VDWAALS = 0.0000 EEL = -3355.8325 ERF =
> -3355.8325
> 1-4 VDW = 777.0003 1-4 EEL = 9849.1122 RESTRAINT =
> 0.0000
>
>
> 

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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