On Tue, Apr 7, 2015 at 11:15 AM, Wong, Sook (NIH/NCATS) [V] <
sook.wong.nih.gov> wrote:
> Hi again,
>
> I am trying to generate the parameters for attached PDB without success as
> my command line is showing below:
>
> FATAL: Atom .R<POT 4875>.A<POT 1> does not have a type.
> FATAL: Atom .R<POT 4876>.A<POT 1> does not have a type.
> FATAL: Atom .R<CLA 4877>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4878>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4879>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4880>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4881>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4882>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4883>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4884>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4885>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4886>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4887>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4888>.A<CLA 1> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
> Can anyone explain how to resolve this problem? Appreciated.
>
It looks like you created this PDB file using CHARMM tools. In
particular, CHARMM names their potassium ion POT and chloride CLA. But
Amber rather sensibly follows the PDB standard for these names. So you
will need to change the residue and atom names of POT and CLA to K and CL,
respectively in the PDB file.
Googling the error messages (e.g., "FATAL: Atom does not have a type
Amber") also likely gives you helpful past threads on this (common) error
message.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Apr 07 2015 - 09:00:05 PDT
