Re: [AMBER] LeAP and FFs for Hybrid DNA/RNA structure

From: David Case <>
Date: Sat, 18 Feb 2017 15:33:35 -0500

On Fri, Feb 17, 2017, Kasprzak, Wojciech (NIH/NCI) [C] wrote:
> I am trying to run an Amber 14 MD simulation (explicit solvent, PME
> and/or implicit solvent GB-neck2) of a hybrid nucleic acids structure
> of 4 chains (2 DNA, 2 RNA) forming two DNA/RNA helices and one all-DNA
> helix.
> I built two sets of parameter files (incl. water box and ions), one
> based on leaprc.ff14SB ONLY (plus frcmod.ionsjc_tip3p) and the other
> with leaprc.ff14SB AND leaprc.parmbsc0_chiOL4_ezOL1.
> I can immediately see that the DNA atoms in an output PDB files have
> different names for the dual ff LEaP, and there are numerous differences
> in the topology parameters files.

Can you provide an example of the name differences? We re-worked the
nomenclature for force fields in 2016 (for AmberTools16), and it's a little
hard to go back to figure out how things used to be. I had thought that
all our files had used IUPAC/PDB names for nucleic acids for some time.

> 1. Which is the correct (or better) way of preparing a DNA/RNA
> simulation, and what is the meaning of a warning in the Amber 14 manual
> (section 3.2.2) regarding the chi (chiOL4) modifications and shared
> naming conventions for RNA and DNA.

This, I think, has to do with atom *types*, not atom names; but atom types
don't appear in PDB files.

I'll leave it up to others to comment on any potential problems with DNA/RNA

> 2. Can the same LEaP approach be applied to implicit solvent simulations
> (GB-HCT igb=1 & mbondi and/or Gb-neck2 ibg=8 & mbondi3)?

You need to either specify the PBRadii to be used at the time LEAP is run, or
use ParmEd to change the radii after the fact. The igb choice is made at the
time sander or parmed is run.


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Received on Sat Feb 18 2017 - 13:00:02 PST
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