On Tue, Nov 22, 2011 at 5:41 PM, Crystal.CHIA-YU Ku <
crystal.chia.yu.gmail.com> wrote:
>
> Probably the library all_nucleic94.lib includes the complete information of
> hydrogen and other atoms of base and sugar, so xleap can add hydrogen and
> base once it detects no hydrogen and no base information of defect
> residues. I think for my case, I have to handle receptor + metal, and
> ligand separately, then merge them together into one pdb for MD simulation.
>
Keep in mind that all_nucleic94.lib applies to the "old" PDB format
standard. All modern PDB files use a different naming scheme (that's
reflected in nucleic10.lib) that could cause problems. This might be the
source of your error.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Nov 23 2011 - 09:00:03 PST
