Re: [AMBER] Protein-DNA covalent bond

From: David A Case <>
Date: Fri, 11 Oct 2013 10:39:12 -0400

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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Received on Fri Oct 11 2013 - 08:00:03 PDT
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