Thanks again, Dr. Baker. 

I will have to check why my calculations take so much time. 

The parameters I chose are the suggested values from your PNAS article and from the discussions in the APBS user list. They are: 
        
         grid 0.1 0.1 0.1
        mol 1
        srfm sacc
        swin 0.3
        srad 1.4
        press 0.2394
        gamma 0.0209
        bconc 0.03348
        sdens 10.0
        dpos 0.2
        temp 300.00
        calcenergy total
        calcforce no

Do you think I must optimize these parameters for my system (protein-DNA complex; ~9000 atoms) by benchmarking it against explicit solvent calculations? 

Will be grateful for any suggestions or pointers. 

Thank you, 
Sincerely, 
Vignesh

On Mon, Nov 29, 2010 at 1:53 AM, Baker, Nathan <Nathan.Baker@pnl.gov> wrote:
Hi Vignesh --

There shouldn't be a huge difference in time; the computational complexity for the SAV and WCA calculations is approximately linear.

The energy differences likely arise from the parameters you've chosen for gamma, pressure, and the probe radius.  How did you select these parameters?

Thanks,

--
Nathan Baker
Pacific Northwest National Laboratory
(509) 375-3997
________________________________________
From: Vigneshwar Ramakrishnan [vmsrvignesh@gmail.com]
Sent: Saturday, November 27, 2010 5:56 PM
To: Baker, Nathan
Cc: apbs-users@lists.sourceforge.net
Subject: Re: [Apbs-users] ERROR: initAPOL: Got NULL Vparam object!

Thanks, Dr. Baker.

May I please also ask if including the WCA energy calculation will take enormous time ?
I did a test calculation with ~800 atoms and it took about 1.5 hours. Another calculation with ~9000 atoms has been running for about ~15 hours now and has not yet ended. I just want to know if I am right, or I have made some mistake somewhere unknowingly.

Also, for the 800 atom system, the total apolar energy is about ~2000 kJ/mol with WCA model and ~3000 kJ/mol with the SAV model (that is, only gamma and press keywords; bconc set to 0). Can I please check with you if such a huge difference is expected (1000kJ/mol)? From the PNAS article  (http://www.pnas.org/content/103/22/8331.full) I understand that the SAV model significantly brings the apolar solvation energies closer to the explicit solvent calculations. If the SAV model is accurate enough (despite the large difference introduced by WCA model), then, in light of the time-consuming nature of the WCA calculations, can I rely just on the calculations based on the SAV model? (I am interested in calculating the relative binding energies of the wild type and mutant protein-DNA system.)

I will be glad to for any pointers and suggestions.

Thanks very much,
Sincerely,
Vignesh



On Sat, Nov 27, 2010 at 11:30 PM, Baker, Nathan <Nathan.Baker@pnl.gov<mailto:Nathan.Baker@pnl.gov>> wrote:
Great; I'm glad it's fixed!

--
Pacific Northwest National Laboratory
(509) 375-3997
________________________________________
From: Vigneshwar Ramakrishnan [vmsrvignesh@gmail.com<mailto:vmsrvignesh@gmail.com>]
Sent: Saturday, November 27, 2010 12:08 AM
To: apbs-users@lists.sourceforge.net<mailto:apbs-users@lists.sourceforge.net>
Subject: Re: [Apbs-users] ERROR: initAPOL: Got NULL Vparam object!

Dear All,

Sorry, I realized that this error was because I hadn't given the parameter file. The latest version (1.3) gave me the detailed error.

Thanks very much,
Vignesh

On Fri, Nov 26, 2010 at 8:04 PM, Vigneshwar Ramakrishnan <vmsrvignesh@gmail.com<mailto:vmsrvignesh@gmail.com><mailto:vmsrvignesh@gmail.com<mailto:vmsrvignesh@gmail.com>>> wrote:
Dear All,

I am trying to calculate the nonpolar contribution for a protein-DNA system and I got the following error. I am attaching the input file that I used as well. Could you please give me some pointers as to what this error means? Thanks very much.

Parsed input file.
Got paths for 3 molecules
Reading PQR-format atom data from mon1.pqr.
 8222 atoms
 Centered at (4.971e+01, 4.898e+01, 5.001e+01)
 Net charge -4.00e+00 e
Reading PQR-format atom data from mon2.pqr.
 828 atoms
 Centered at (4.215e+01, 3.732e+01, 4.989e+01)
 Net charge -2.40e+01 e
Reading PQR-format atom data from comp.pqr.
initAPOL:  Got NULL Vparam object!
Error calculating apolar solvation quantities!
 9050 atoms
 Centered at (4.971e+01, 4.898e+01, 5.001e+01)
 Net charge -2.80e+01 e
Preparing to run 3 PBE calculations.
----------------------------------------
CALCULATION #1 (mol1): APOLAR
finished processing 0


----------------------------------------------------------------------

Sincerely,
Vignesh


--
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White)



--
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White)



--
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White)



--
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White)