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
Received on Wed Feb 12 2003 - 12:49:01 PST
