Re: [AMBER] Are RNA with ligand system and a GB neck2 protocol compatible

From: Hai Nguyen <>
Date: Tue, 24 Oct 2017 22:31:20 -0400

On Tue, Oct 24, 2017 at 1:57 PM, Kasprzak, Wojciech (NIH/NCI) [C] <> wrote:

> Dear Amber Users,
> Over the last year I became comfortable with the GB neck2 results for
> RNA-only simulations,
> even though we still run explicit solvent simulations in parallel. Now, I
> have tried for the first
> time an RNA fragment with a small molecule for which the partial charges
> and the parameters
> were derived via Amber 14 antechamber and parmcheck (PDB to MOL2, then
> FRCMOD and PREP files).
> LEAP accepted these files together leaprc.gaff, leaprc.ff14SB and with
> "set default PBradii mbond3"
> for in igb=8 / mbondi3 run. PMEMD.cuda runs well, but we see a lot more
> RNA motion with one of the
> tested ligands than we have seen for the RNA alone. This is either very
> interesting or seriously off.
> Do you have any recommendations for or against GB neck2 runs of RNA with
> ligands? The Sustiva-RT
> tutorial (Amber tutorial 4B) does not rely on explicit solvent, but the
> receptor there is a protein...

> Hoping to hear from anybody who tested the above combination.
> Best regards, Voytek Kasprzak

hi, sounds like you're very first person trying this.
We only tested the simulation with the binding of a ligand to minor groove
of the DNA duplex (saw the rebinding if taking the ligand out of the pocket
from x-ray structure; but this won't tell anything)


> Wojciech (Voytek) Kasprzak (Contractor)
> Analyst Programmer
> Frederick National Laboratory for Cancer Research
> Leidos Biomedical Research, Inc.
> Post Office Box B
> Frederick, Maryland 21702
> Phone: 301-846-5537
> _______________________________________________
> AMBER mailing list
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Received on Tue Oct 24 2017 - 20:00:02 PDT
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