[AMBER] attaching a residue to DNA

From: Daniel Konstantinovsky <daniel.konstantinovsky.yale.edu>
Date: Sun, 9 Jan 2022 08:37:22 -0500

Hello Amber,

I am trying to bond a fatty acid phosphate to a DNA molecule in tleap. The
residue needs to bind to the O5' oxygen on the DNA's first residue. The
problem is, there's a hydrogen (HO5') there already and tleap complains
with "Message: bondAtomProblem found" and "Bond: Maximum coordination
exceeded on .R<MOL 7>.A<H1 20>". I'm guessing this is because of the
hydrogen. Is there a way to bond the residue's P atom to the DNA's O and
get rid of the H in tleap? I can't get rid of the hydrogen or tleap will
complain about missing atoms I think. The fatty acid residue was
parameterized to have the same charge as the HO5' atom to keep everything

Below is my tleap file. STE is the residue I want to bind.

How can I do this and build a topology successfully?

Thank you!

source leaprc.DNA.OL15
source leaprc.water.tip4pew

loadamberparams C18_alone.frcmod
loadoff STE.off

mol = loadpdb STE_phos_3mer_conect.pdb
bond mol.247.P mol.2.O5' 1

solvatebox mol TIP4PBOX 15.0
addions mol Na+ 0

savepdb mol test_water.pdb
saveamberparm mol test_water.prmtop test_water.inpcrd

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Received on Sun Jan 09 2022 - 06:00:02 PST
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