Hi Jason,
Thank you for your important reminding. Could you let me know when pdb
changed their naming scheme? I googled naming scheme change but there is no
clear result about when PDB uses the different naming scheme. Knowing when
PDB uses the different naming scheme helps me to choose proper nucleic acid
library to let xleap understand my pdb file. I think this time that my
problem can be solved by loading the original structure file without adding
H is partially based on the fact, the file is old, obtained in 2006. It
could use the old naming scheme, so all_nucleic94.lib understands bases
inside.
Thank you again for your generous help and information.
Sincerely,
Crystal
On Wed, Nov 23, 2011 at 8:38 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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 - 16:30:03 PST
