AMBER Archive (2003)

Subject: Re: delphi and charge file

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Wed Feb 12 2003 - 16:43:39 CST

Hi Sue,

the message below just says that there are more charge entries in the
charge file than your current delphi version can accept. Increase ncmax
in the line "parameter (ncmax = 2000)" in the file "qdiffpar5.h" in your
delphi src directory (my delphi version is an older one, so there might
be some differences to yours) and recompile delphi or remove non
necessary charge entries from the file.

Best regards

Holger

> Dear amber users:
> I am trying to use delphi in mm_pbsa without much luck. I can run the example in mm_pbsa/Examples/Binding_Stability of amber7 but when I try to run it with my files I get 0 for the pb energy so I modified one of the examples (that come with delphi)and I get the following output:
> __________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 Wed Feb 12 2003
>
> at 14:38:24
>
> opening parameter file param_2_sue
>
> atom radii read from file
>
> /disk03/usr/local/amber7/src/mm_pbsa/Examples/my_parse_delphi.siz
>
>
>
> !my siz based on PARSE
>
> !(value for P taken from Pauling,
>
> ! for Mg from Biophys J 2001, 80, 1151)
>
> # of radius parameter records: 10
>
>
>
> atomic charges read from file
>
> /disk03/usr/local/amber7/src/mm_pbsa/Examples/amber94_delphi.crg_4
>
>
>
> !Amber parm94 charges
>
> maximum # of charge records exceeded
>
> - increase ncmax
> It seems the problem is with the charge file, does anyone have any suggestions?
> Thanks in advance,
> Sue Heavner 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++