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

From: Kasprzak, Wojciech (NIH/NCI) [C] <"Kasprzak,>
Date: Mon, 20 Feb 2017 18:36:18 +0000

Dear Dr. Case,

Thank you for your answer about the FFs and DNA/RNA complexes. The bottom line is, I gather,
that I should use both RNA and DNA parameters and that, in principle they can be employed with GB-neck2
after proper PBradii are set.

I apologize for my delayed response. I did not have full access to all the data over the weekend.
I retested leap sessions in Amber 14 environment on two machines (separate campuses and administrators),
and they both yielded identical PDB and PRMTOP output after leaprc.ff14SB & leaprc.ff14SB AND leaprc.parmbsc0_chiOL4_ezOL1
were sourced (DNA chains have phosphate groups with P, O1P and O2P atom names and are capped by H5T & H3T, while
RNA chains use PDB 3.x standard).

One of our systems has Amber 16 installed and leap returns uniform atom names for DNA and RNA (P, OP1, OP2 and HO5'
and HO3' respectively) after leaprc.RNA.OL3 and leaprc.DNA.OL15 are sourced. Unfortunately I ran into
some criptic failure after the" addions mol Na+ 0" command and could not produce PRMTOP file for comparison with
the previously created Amber 14 equivalent. (I will have to resolve this issue with our scientific apps administrators,
since that was never a problem in the past.)

If anybody can offer comments or warnings about RNA/DNA simulations, I will appreciate it very much.

Best regards, Voytek Kasprzak

Wojciech (Voytek) Kasprzak (Contractor)
Analyst Programmer,
Basic Science Program,
Leidos Biomedical Research, Inc.
Frederick National Laboratory for Cancer Research (FNLCR)
Frederick, MD 21702
(301) 846 5537

From: David Case []
Sent: Saturday, February 18, 2017 3:33 PM
To: AMBER Mailing List
Subject: Re: [AMBER] LeAP and FFs for Hybrid DNA/RNA structure

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 Mon Feb 20 2017 - 11:00:02 PST
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