No Jason, I don't get this warning because I get the error and the
program crashes beforehand ...
Vlad
On 08/07/2012 04:21 PM, Jason Swails wrote:
> 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
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 07 2012 - 08:00:03 PDT
