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

From: Kasprzak, Wojciech (NIH/NCI) [C] <"Kasprzak,>
Date: Tue, 24 Oct 2017 17:57:29 +0000

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

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

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Received on Tue Oct 24 2017 - 11:00:03 PDT
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