AMBER Archive (2004)

Subject: Re: AMBER: question about delphi and UHBD

From: xhu1_at_memphis.edu
Date: Thu Sep 30 2004 - 11:52:01 CDT

Dear Dr. Cheatham,

I tried Na+ and one amino acid GLN using amber7 parameters(parm94.dat
xxx94.lib). internal/external dielectric constants are 1.0/80.0,;
T=298K; grid dimension 160X160X160; boundary potentials are
approximated by the Debye-Huckel potential, no focusing. The results
are:

1. Na+
   a). grid space= 1A
       UHBD: -89.37 kcal/mol
       delphi: -87.85 kcal/mol
   
   b). grid space=0.25 A
       UHBD: -87.88 kcal/mol
       delphi: -87.85 kcal/mol

2. GLN
   a). grid space= 1A
       UHBD: -23.16kcal/mol
       delphi: -23.14kcal/mol
   
   b). grid space=0.25 A
       UHBD: -22.20kcal/mol
       delphi: -21.54kcal/mol

I also tried grid dimension 80X80X80, which does not affect the
results at all. Then, I tried a protein with 99 residues under the
same conditions as Na+ and GLN run. The results are:

grid space = 1.0 A, no focusing
UHBD: -1542.5 kcal/mol
delphi: -1217.1 kcal/mol

grid space = 0.25 A, focusing
UHBD: -1466.0 kcal/mol
delphi: -1035.7 kcal/mol

  
For small systems like Na+ and GLN, the results from both programs are
kind agree: Na+ at grid space 0.25A; GLN at grid space 1.0A. However,
for a large system, the difference is large, looks like. Because I
can't get a number around -97 for Na+ as you mentioned, I attached the
input and output files of Na+ and GLN running here. Could you please
take a look for me if you have a time? Thank you so much

Regards

Shawn

----- Original Message -----
From: "Thomas E. Cheatham, III" <cheatham_at_chpc.utah.edu>
Date: Tuesday, September 28, 2004 1:34 pm
Subject: Re: AMBER: question about delphi and UHBD

>
> Dr. Luo wrote:
>
> > Aside from different numerical implementations of molecular
> surface and
> > finite difference solvers, Delphi and UHBD also use very different
> > methods to compute reaction field energies. So in the end, you
> can't get
> > agreement at all for a complex molecule, such as a large protein.
>
> From the original e-mail of Shawn:
>
> > The final solvation energies for ligand, receptor and complex are
> > -1466, -1529 and -2730 kcal/mol in UHBD and -1035, -1056, -1224
> > kcal/mol in delphi.
>
>
> Despite the different algorithms used and the size of the systems
> beingstudied, I find it rather difficult to believe that these
> differences in
> energetics are reasonable between the two programs. One program
> suggestsa free energy difference of 265 kcal/mol and the other 867
> kcal/mol for
> the complex - (receptor + ligand) favoring the separated proteins.
> Both
> of these are completely unreasonable (if they are the final solvation
> energies). The disagreement between the two methods makes me
> wonder if
> the numbers are indeed comparable. Do the continuum solvation
numbers
> include anything else that you do not realize? Is the conversion
from
> reaction field energy to kcal/mol correct? Are both running with
> the same
> internal dielectric? Even generalized Born and continuum methods, in
> general, show better agreement than is seen between UHBD and
> delphi shown
> above leading me to speculate that something is amiss either in the
> running or interpretation of the results. I do not think this
> relates too
> heavily to the number of iterations.
>
> To test out your knowledge of delphi and UHBD, try running a
> really simple
> test case, like a continuum run on an isolated Na+; both programs
> shouldgive a number around 97 or so for the Na+ parameters (Aqvist
> adapted)present in AMBER.
>
> Good luck.
>
> -------------------------------------------------------------------
> ----
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>


  • application/octet-stream attachment: gln.rar

  • application/octet-stream attachment: Na.rar

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu