Thanks for your reply. I also noticed that DIME parameters are exactly the same for several mesh size for 1AJJ (279 atoms), but for large molecules such as 1A7M(2803 atoms) the DIME parameters are different for mesh size 1.0, 1.2 and 1.5 (but,NOT all x, y and z). For example, these parameters are as following for 1A7M (only x of dime is different):
1a63.1.5.in:
    mg-manual
    dime 33 33 33
    nlev 4
    glen 106.275 64.289 65.372
1a63.1.2.in:                                                                                                             
    mg-manual
    dime 65 33 33
    nlev 4
    glen 106.275 64.289 65.372

This makes me somewhat confused: it seems that the key parameters in APBS are "dime" and "glen", but not mesh size! And parameter file generated by "inputgen.py" do not really reflect the given "space"? ---- Does my understanding right?


2009/7/20 Yong Huang <yhuang01@gmail.com>
Hello,

I think the differences in APBS results indicate the differences in the grid points of your calculations. I am just recapping the differences from your input files:

Fine mesh resolution                   dime
        1.5                                    33 33 33
        1.2                                    33 33 33
        1.0                                    33 33 33
        0.8                                    33 33 33
        0.6                                    65 65 65
        0.5                                    65 65 97
        0.4                                    97 97 97
        0.3                                    129 129 161

Here 33 33 33 are the smallest grid points we can have for a mg-manual calculation, that's why when you chose fine grid resolutions > 1.0 Angstroms, APBS grid points couldn't go any lower than 33 33 33. As a result, your APBS calculation results for grid resolution > 1.0 remained the same (based on dime 33 33 33).

Thanks, 

Yong


2009/7/20 Nathan Baker <baker@biochem.wustl.edu>
Hello -

I'm traveling right now but will ask Dave Gohara and Yong Huang to look into this while I am gone.  This is very strange...

Thanks,

Nathan












On Jul 20, 2009, at 3:19 AM, Ƹ wrote:

Doctor Baker:
Thank you. I check my .in files and find out that 1ajj.in are exactly the same with the space parameters 0.8,1.0,1.2,1.5(many other pdb are the same )
My apbs input file is made manually following  the user manual of APBS
the command  are as below:(for space is 1.0 angstrom)
inputgen.py --space=1.0  --method=manual 1ajj.pqr
 
2009/7/16 Nathan Baker <baker@biochem.wustl.edu>
Hello --

That is very strange; not at all what I would expect from these calculations.  Would you mind sending the PQR and input file so I can see how you've set the problem up?

Thanks,

Nathan

On Jul 15, 2009, at 10:08 PM, Ƹ wrote:

APBS USERS:
 
I have calculated the solvation energy of  20 PDB molecules with APBS, and  use different  mesh size .
The results turn out to be exact the same when the mesh size are  1.5  1.2  1.0  0.8 angstrom on most molecules.
 
I wonder why is it?
Is APBS consider any mesh size bigger than 1.0 angstrom as 1.0 angstrom ?
 
IF you know it ,please tell me! Thank you very much!
 
PS: the results of 1ajj (PDB ID)
 
Pdb
software
1.5
1.2
1
0.8
0.6
0.5
0.4
0.3
0.2
1ajj
APBS
-539.42
-539.42
-539.42
-539.42
-564.49
-563.7
-558.31
-554.42
-551.52
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--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Director, Computational and Molecular Biophysics Graduate Program
Center for Computational Biology, Washington University in St. Louis













--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Director, Computational and Molecular Biophysics Graduate Program
Center for Computational Biology, Washington University in St. Louis















--
Yong Huang, D.Sc.

Center for Computational Biology
Washington University School of Medicine