On Fri, Sep 18, 2015 at 6:31 AM, Urszula Uciechowska <
urszula.uciechowska.biotech.ug.edu.pl> wrote:
> Dear Amber users,
>
> From the MMPBSA.py run I obtained an error:
>
> No radius assigned for atom 4675 C5' CI
>
> I am trying to use parmed.pt to change it by typing:
>
>
> Choose an Amber Topology file to load: complex.prmtop
> Loaded Amber topology file complex.prmtop
>
> Reading input from STDIN...
> > change AMBER_ATOM_TYPE .%CI C
> MaskError: AmberMask: Bad syntax
>
> what is wrong here?
>
As the error message states, .%CI is not a valid Amber mask -- the period
is not a character used in the Amber mask syntax. What made you think it
was? If it's mistaken documentation, it would be nice to fix it to avoid
this misunderstanding in the future.
The character you're looking for is @, not .
change AMBER_ATOM_TYPE .%CI C
You can find a more thorough discussion of Amber masks here:
http://parmed.github.io/ParmEd/html/amber.html#amber-mask-syntax
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Sep 18 2015 - 05:00:05 PDT
