Re: [AMBER] DNA Phosphate error

From: Daniel Roe <>
Date: Sat, 27 Jul 2013 10:58:42 -0600


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

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.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Sat Jul 27 2013 - 10:00:04 PDT
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