re: leap adding terminal phosphates

From: Bill Ross <>
Date: Mon 5 Mar 2001 12:27:27 -0800 (PST)

        When I load a DNA:protein complex into LEaP starting with an NMR
        structure that has 5' and 3' hydroxyl termini, the program adds
        an incomplete phosphate (PO2) to the 5' ends and leaves a dangling
        oxygen (unprotonated) at the 3' ends. Here is an excerpt of the output:
          Added missing heavy atom: .R<DA 30084>.A<P 1>
          Added missing heavy atom: .R<DA 30084>.A<O1P 2>
          Added missing heavy atom: .R<DA 30084>.A<O2P 3>

Assuming a TER card follows each molecule in the pdb file,
this can be solved by the general method of using the addPdbResMap
command as in the default leaprc to force terminal residues to be
converted to the canonical terminal type.

The other way is to rename the residue in the pdb file, in this
case DA -> DA3.

Bill Ross
Received on Mon Mar 05 2001 - 12:27:27 PST
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