Re: [AMBER] Protein-DNA covalent bond

From: John Gehman <>
Date: Sat, 12 Oct 2013 07:53:12 +0000

Many thanks Dave,

Indeed, the prmtop files were fine; I was processing in tleap in two stages, connected by an ambpdb-generated PDB file in between, and that was the weak link (pun acknowledged). The second stage tleap didn't have the bond information from the intermediate PDB file to work with, hence my DNA dissociated from the complex during slow heating.

It was Chimera that was being asked to guess at the bonds without the CONECT information in the intermediate PDB file. Using VMD (and confirmed that the prmtop files were correct.

Sorry to take your time for an elementary error, but many thanks for straightening me out!

Kind Regards,

John Gehman
ARC Future Fellow
School of Chemistry
Bio21 Institute
Univ. of Melbourne VIC 3010
+61 3 8344 2417
From: David A Case []
Sent: Saturday, 12 October 2013 1:39 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Protein-DNA covalent bond

On Fri, Oct 11, 2013, John Gehman wrote:
> I need to form a covalent bond between a serine and a 5' phosphate on
> a DNA strand.
> 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).

What do you mean by "per the resulting pdb file"? You can use rdparm or
ParmEd to examine the bonds that are in the prmtop file, or you can visaully
do this in VMD by loading the prmtop file first.

But pdb files themselves don't contain bonding information; I'm guessing(?)
that you might be using a visualization program, but these have to guess where
the bonds are, and sometimes guess wrong.


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