Hello amber users,
I have a problem with my MM/PBSA calculations.
When I do the calculation using MM/GBSA (without Delphi), I obtain a value of
GB that it is not 0.0. So, the MM/GBSA calculation goes right.
Nevertheless, when I run a MM/PBSA using AMBER7 and Delphi, I obtain the value
of PBCAL is 0.0.
The delphi.log files that I obtain are like this:
(my system has 150 atoms)
___________________________________________________
___________________DelPhi II____________________
/ \
| A program to solve the PB equation |
| in 3D, using non-linear form, incorporating |
| 2 dielectric regions, ionic strength, 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 |
\__________________ ____________________/
DelPhi II
program started on Thu Jan 13 2005
at 19:02:57
opening parameter file delphi.prm.0
atom radii read from file
./HHH.siz2
!my siz based on PARSE
!(value for P taken from Pauling,
! for Mg from Biophys J 2001, 80, 1151)
# of radius parameter records: 150
atomic charges read from file
./HHH.crg2
! Amber parm99 charges
# of charge parameter records: 150
assigning charges and radii...
opening formatted file:fort.13
number of atoms read in = 0
exiting due to non-existence of atom file
_______________________________________________
I have read Delphi manuals and I know that fort.13 is a file with pdb format.
I've read in AMBER7 manual about mm/pbsa and it doesn't talk about we have to
use a pdb file in mm_pbsa.in.
Maybe there are some bugs in the mm_pbsa.pl I have (ver. 1/16/2002 ). Do you
know if there is a new version of mm_pbsa.pl ?
If someone can help me, I accept any suggestion.
Thanks in advance,
Xavi
Javier Perez
Grup de Química Orgànica Estructural
Departament de Química
Universitat Autònoma de Barcelona
08193 Bellaterra-Espanya
Lab.: C7-455
Tel.: +34 935811266
http://einstein.uab.es/cjaime/
http://www.gratisweb.com/xavip/
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Received on Thu Jan 13 2005 - 21:52:59 PST
