Hi,
The way I would do this would be to create a whole library for the modified
5'residue, but the tutorial here has instructions for modifying the 5' end
of DNA:
http://ambermd.org/tutorials/advanced/tutorial1/section4.php
-Christina
On Sun, Jan 9, 2022 at 8:37 AM Daniel Konstantinovsky <
daniel.konstantinovsky.yale.edu> wrote:
> 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
> even.
>
> 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!
> Dan
>
> 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
>
> quit
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-----------------------------------------------------------------
Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
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Received on Mon Jan 10 2022 - 06:30:03 PST
