[Chimera-users] generating electrostatic potential map

[Elaine Meng]

Hi Bala,
This error occurs in DelPhi (not in Chimera) and is apparently  
because the format of the radius file is wrong.  It looks like   
DelPhi is expecting a different line at the top of the radius file.   
I looked at the "default.siz" file in our local installation of  
DelPhi, and it has this line before the radius parameters:

atom__res_radius_color_

You could try putting that line or even a blank line at the top of  
your radius file, but probably the best thing to do is check the  
description of this file format in the DelPhi manual.
I hope this helps,
Elaine

On Oct 27, 2006, at 7:43 AM, bala wrote:

> Hello all,
>
> I want to generate the electrostatic potential map using Chimera. I  
> tried through Delphi controler, however i am repeatedly getting an  
> error as follows. I have successfully installed Delphi. Can someone  
> suggest me what is wrong.
>
>   __________DelPhi V. 4 Release 1.1 ______________
>  |                                                |
>  | A program to solve the PB equation             |
>  | in 3D, using non-linear form, incorporating    |
>  | many dielectric regions, multisalt ionic       |
>  | strength, different probe radii, periodic      |
>  | and focussing boundary conditions, utilizing   |
>  | stripped optimum successive over-relaxation    |
>  | and an improved algorithm for mapping the      |
>  | Mol. Surface to the finite-Difference grid     |
>  | Recompiled on Linux and PC                     |
>  |    January 2002 --------  Walter Rocchia       |
>  |__________________           ___________________|
>                     DelPhi V. 4
>
>   program started on Fri Oct 27 2006
>               at 14:55:00
>  opening parameter file /tmp/tmpvpgS8V
>  At least 30 nonlinear iterations
>  atom radii read from file
>  /usr/people/ojha/BALA/chim_amber.siz
>
>  unknown header format in radius file:
>   O5' A     1  1.7210
>
> First it showed the same for H5 atom [which was the first atom in  
> the siz/charge file], then i just tried by deleting the first line  
> in the radius and charge file. Then the same error is coming for  
> the second atom O5' in the file.
>
> Thanks in advance,
> Bala
>
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-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




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