[AMBER] Protein-DNA covalent bond

From: John Gehman <jgehman.unimelb.edu.au>
Date: Fri, 11 Oct 2013 00:51:55 +0000

Dear Amber users,

I would be most grateful if anybody could straighten me out here ...

I need to form a covalent bond between a serine and a 5' phosphate on a DNA strand. In fact there are four such instances in the molecular complex that I'm trying to set up prior to MD etc. I have created the PS5-DA connection for input into tleap with Chimera, and confirmed that the CONECT information includes the covalent bonds in question.

I've got all the ff/lib/off/frcmod jazz sorted, where I
-- adapted phosphoserine parameters that I found to create a new "PS5" ("Phospho-Serine-5'") residue to substitute for serine in the protein chains
-- commented out the following lines within addPdbResMap, in amber12/dat/leap/cmd/leaprc.ff12SB (per previous guidance in this list from Dave Case)
  # { 0 "DG" "DG5" } { 1 "DG" "DG3" }
  # { 0 "DA" "DA5" } { 1 "DA" "DA3" }
  # { 0 "DC" "DC5" } { 1 "DC" "DC3" }
  # { 0 "DT" "DT5" } { 1 "DT" "DT3" }
-- manually edited the PDB file to use DN5 and DN3 for the DNA termini at the *other* ends than those with covalent connection to my PS5 residues, and kept the 5' end that is connected as "DA"
-- include the gaff ff in the tleap setup.

This enables successful processing and writing of prmtop and inpcrd. I note that *before* I sorted out those steps above, I would get errors about missing angle and dihedral information, due to the unnatural CA-OG-P connectivity in the molecule. This would seem to indicate that the desired covalent bonds are indeed recognized (up to a point) in tleap.

HOWEVER, the PS5-DA covalent bonds don't seem to survive through to saveAmberParm, per the resulting pdb file written from these output files using ambpdb (nor with savePDB within tleap). If I include an additional four lines in the tleap script:
bond GD.10.OG GD.386.P
bond GD.193.OG GD.456.P
bond GD.516.OG GD.421.P
bond GD.699.OG GD.491.P
I get a complaint that these are redundant with CONECT statements in the PDB file. If I then manually remove the offending CONECT combinations in the PDB file and try to let tleap handle it instead, everything passes and output files get written, but still, again, the PS5-DA covalent bond are missing.

Clearly I'm still missing something, but what?

Many thanks for your help.

Kind Regards,
John Gehman
ARC Future Fellow
School of Chemistry
Bio21 Institute
Univ. of Melbourne VIC 3010
+61 3 8344 2417

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Received on Thu Oct 10 2013 - 18:00:03 PDT
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