AMBER Archive (2003)

Subject: delphi and charge file

From: Sue Heavner (sheavner_at_hsc.wvu.edu)
Date: Wed Feb 12 2003 - 14:49:01 CST

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