Hi,
When I try to load the PDB file you provided into tleap, I receive the
following message:
Loading PDB file: ./new_dna-edited.pdb
(starting new molecule for chain H)
Created a new atom named: P within residue: .R<DG5 2>
Created a new atom named: O1P within residue: .R<DG5 2>
Created a new atom named: O2P within residue: .R<DG5 2>
total atoms in file: 387
Leap added 216 missing atoms according to residue templates:
216 H / lone pairs
The file contained 3 atoms not in residue templates
This is because in your first NA residue in the PDB (which by
convention is the 5' terminal residue for the first strand) you have
entries for a phosphate group, which according to residue templates
the 5' terminal residue should not contain. If you remove the entries
for the P, O1P, and O2P atoms of residue DG:2 the PDB will load
correctly.
It seems like this error occurred because there was (or should be) a
residue 1 that is the actual 5' terminal residue - if your structure
requires this residue you may need to build it in.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jul 27 2013 - 10:00:04 PDT
