AMBER Archive (2008)

Subject: Re: AMBER: problem with running mm-pbsa

From: Ray Luo (rluo_at_uci.edu)
Date: Fri Oct 24 2008 - 11:24:59 CDT

Could you be more specific?

Which amber distribution?
What is your input?
Where did you find your patch?

All the best,
Ray

On Fri, Oct 24, 2008 at 12:14 AM, <moitrayee_at_mbu.iisc.ernet.in> wrote:
> 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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