Hello --

This protein (R67 DHFR) is a perfect D2 symmetric protein.
Dr. Howell used the Delphi program to get the potential map before and it's symmetric. (attachment "delphi potential.jpg")
But the potential map we got is not symmetric. (attachment "apbs potential.jpeg" front and back)
There are two major unsymmetric parts, the two N-terminal and two C terminals.
We have been stuck here for quite a while and don't know which step was wrong.

Did you use all the same parameters (e.g., charges and radii) with APBS as you did with DelPhi?  What biomolecular surface definitions did you use for both programs?  What was the grid spacing in your calculation?

Thanks,

Nathan

Really wish we could get your help on this.
Thanks a lot.
 
 
ps: I use the apbs.in generated by the webserver and use apbs 0.5.0 to get the .dx file.
     and load .pqr and .dx in VMD 1.8.6, color scale -10 to 10.


Chuanyin Shi
Department of Chemistry & Biochemistry
Old Dominion University
Norfolk, VA 23529
Cell:  (757) 553-1204
e-mail:  cshi@odu.edu

-----sobolevnrm@gmail.com wrote: -----

To: "Chuanyin Shi" <CShi@odu.edu>
From: "Nathan Baker" <baker@ccb.wustl.edu>
Sent by: sobolevnrm@gmail.com
Date: 10/26/2007 03:25PM
cc: "Yong Huang" <yhuang01@gmail.com>, "David Gohara" <sdg0919@gmail.com>
Subject: Re: question about PDB2PQR

Hello --

Unless the monomers of the tetramers are perfectly symmetric (unlikely
for a crystal structure), then there should be some asymmetry.  Can
you send a picture of the asymmetry that you're worried about?

Thanks,

Nathan

On 10/24/07, Chuanyin Shi <CShi@odu.edu> wrote:
> Dr. Baker:
>
> This is a graduate student from Old Dominion University.
> I am working on the electrostatic potential for a homotetramer recently.
> But I am having trouble generating a correct potential map.
> Since this is a tetramer, so when I use the PDB2PQR web server,
> I got warning on the terminal residues,
>
>
> REMARK   1 PQR file generated by PDB2PQR (Version 1.2.1)
> REMARK   1
> REMARK   1 Forcefield Used: charmm
> REMARK   1 Naming Scheme Used: charmm
> REMARK   1
> REMARK   5 Gap in backbone detected between ASN A 60 and PRO A 61!
> REMARK   5 Gap in backbone detected between ASN A 120 and PRO A 121!
> REMARK   5 Gap in backbone detected between ASN A 180 and PRO A 181!
> REMARK   5 WARNING: Unable to debump ASN A 60
> REMARK   5 WARNING: Unable to debump ASN A 120
> REMARK   5 WARNING: Unable to debump ASN A 180
> REMARK   5 WARNING: Unable to debump ASN A 60
> REMARK   5 WARNING: Unable to debump ASN A 120
> REMARK   5 WARNING: Unable to debump ASN A 180
> REMARK   5
> REMARK   6 Total charge on this protein: 0.0000 e
> REMARK   6
>
>
> And after got the .pqr file and apbs.in file, i use apbs0.5.0 program to get
> the .dx potential,
> Everything goes well but the potential map is not symmetric as it supposed
> to be.
> I don't know if the gap between monomers matter a lot?
> I wish you could give me a hint on this.
> Thanks in advance.
>
> I've attached the .pdb file in attachment,
> R67 DHFR, homotetramer, 240 residues total, 60 residues each monomer.
>
>
> Chuanyin Shi
> Department of Chemistry & Biochemistry
> Old Dominion University
> Norfolk, VA 23529
> Cell:  (757) 553-1204
> e-mail:  cshi@odu.edu
>
>


--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/

<apbs potential front.JPG><apbs potentian back.JPG><delphi potential.JPG>

--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/