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

From: Kasprzak, Wojciech (NIH/NCI) [C] <"Kasprzak,>
Date: Fri, 17 Feb 2017 20:09:39 +0000

Dear Amber Users,

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.

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.

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

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
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Received on Fri Feb 17 2017 - 12:30:03 PST
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