AMBER Archive (2008)

Subject: AMBER: problem with running mm-pbsa

From: moitrayee_at_mbu.iisc.ernet.in
Date: Fri Oct 24 2008 - 02:14:49 CDT

Dear all,

I was running mm-pbsa calculations on a protein-ligand complex and the job
terminated in a particular snapshot giving the error: PB Bomb in epsbnd(): No
neighbor found for exposed boundary grid 76 110 25

I searched the archive to fix the error using bugfix4 in Amber8. But after
applying the patch when i am trying to re-compile it it gives lots of error as
following and the recompilation is aborted.

In file pb_force.f:149

module poisson_boltzmann
 1
Error: Non-numeric character in statement label at (1)
In file pb_force.f:149

module poisson_boltzmann
 1
Error: Unclassifiable statement at (1)
In file pb_force.f:153

   real (kind=8), parameter :: pbkb = 1.3807D-23 / 1.6606D-27 / (1.00D+
    1
Error: Non-numeric character in statement label at (1)
In file pb_force.f:153

   real (kind=8), parameter :: pbkb = 1.3807D-23 / 1.6606D-27 / (1.00D+
        1
Error: Unexpected array reference at (1)
In file pb_force.f:154

   real (kind=8), parameter :: fioni = 6.0220D+23 / 1.00D+30
    1
Error: Non-numeric character in statement label at (1)
In file pb_force.f:154

   real (kind=8), parameter :: fioni = 6.0220D+23 / 1.00D+30
        1
Error: Unexpected array reference at (1)
In file pb_force.f:155

   real (kind=8), parameter :: fiono = 1.0D0 / fioni
    1
Error: Non-numeric character in statement label at (1)
In file pb_force.f:155

   real (kind=8), parameter :: fiono = 1.0D0 / fioni
        1
Error: Unexpected array reference at (1)
In file pb_force.f:156

   real (kind=8), parameter :: eps0 = 8.8542D-12 / (1.6022D-19)**2 / (1
    1
Error: Non-numeric character in statement label at (1)
In file pb_force.f:156

   real (kind=8), parameter :: eps0 = 8.8542D-12 / (1.6022D-19)**2 / (1
        1
Error: Unexpected array reference at (1)
Fatal Error: Too many errors, aborting.
So what should i do. Please help urgently.
Thanks a lot in advance.

Sincere Regards
Moitrayee Bhattacharyya
Molecular Biophysics Unit
Indian Institute of Science
India. 

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