Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ...

From: Niel Henriksen <>
Date: Tue, 7 Aug 2012 14:30:07 +0000

... just a side note for the developer who does add atom
types eventually to the source code. The bsc0 and OL3
parameters for DNA/RNA require new atom types that need
to be added as well.

From: Jason Swails []
Sent: Tuesday, August 07, 2012 8:21 AM
To: AMBER Mailing List
Subject: Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ...

On Tue, Aug 7, 2012 at 9:53 AM, Vlad Cojocaru <> wrote:

> Jason,
> However, one mistery remains. Why using inp=2 and radiopt=0 still gives
> the same error but inp=1 and radiopt=0 does not ? As far as I got it,
> radiopt=0 should force to read radii from the topology file and
> therefore in should work with any inp value. Or maybe when setting inp=2
> the program overwrites automatically the radiopt=0 from the input file ?

It seems that your latter guess is right. From the PBSA source code:

   if ( inp == 2 .and. radiopt /= 1 ) then
      write(6, *) 'PB Warning in pb_read(): radiopt has been reset to 1
because inp=2.'
      radiopt = 1
   end if

Do you see that warning in the output file? In the long run, I think
modifying the source code to recognize ILDN atom types is the best
solution, but the fix I mentioned previously is a good
workaround for the time being.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Tue Aug 07 2012 - 08:00:02 PDT
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