On Mon, Apr 5, 2010 at 2:47 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
> Hi,
>
> I'm using leaprc.ff99bsc0 and there in the *addPdbAtomMap* column, it is
> written :
>
> { "HO5'" "H5T" }
> { "HO3'" "H3T" }
>
>
> So I have changed HO'5 and HO'3 with H5T and H3T in the RNA pdb file and now
> it is working fine.
>
> Am I right?
Yes. If you look at all_nucleic94.lib in $AMBERHOME/dat/leap/lib, you
will see that the atom name H5T in residue RU5 (5-prime uracil RNA)
corresponds to the atom you're looking for (and likewise for H3T with
RU3). HO'5 and HO'3 are nowhere to be found in that library file, so
they do not map to any atom type (hence the errors you were getting).
All the best,
Jason
>
> Asfa.
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--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Apr 05 2010 - 03:00:02 PDT
