Hello,
On Mon, Feb 1, 2010 at 10:09 AM, Beale, John <John.Beale.stlcop.edu> wrote:
> I am trying to process in leap a protein that is bonded to a short
> single strand of DNA. I am getting FATAL errors that look like this:
>
>
>
> FATAL: Atom .R<DT 262>, A<OP1 33> does not have a type.
>
> FATAL: Atom .R<DT 262>, A<OP2 34> does not have a type.
>
> FATAL: Atom .R<DT 263>, A<OP1 33> does not have a type.
>
> FATAL: Atom .R<DT 263>, A<OP2 34> does not have a type.
>
These are not the correct atom names to be recognized by leap
according to the library files loaded by ff03. Change all instances
of OP1 to O1P, and all instances of OP2 to O2P in your PDB. Then it
should work (unless there are other errors! It will fix the error
messages above though).
The atom names in the PDB must match the atom names in the library
files used. In this case, all_nucleic94.lib (in
$AMBERHOME/dat/leap/lib/).
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Feb 01 2010 - 08:00:02 PST
