Thanks for the suggestion!
Ray
On Tue, Aug 7, 2012 at 7:30 AM, Niel Henriksen <niel.henriksen.utah.edu> wrote:
>
> ... 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.
>
> --Niel
> ________________________________________
> From: Jason Swails [jason.swails.gmail.com]
> 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 <
> vlad.cojocaru.mpi-muenster.mpg.de> 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 xparmed.py fix I mentioned previously is a good
> workaround for the time being.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Aug 07 2012 - 15:30:03 PDT
