Dear Amber Users,
Following the advice from Carlos and Hai on the latest GB-neck2 option for running nuclei acids simulations with
implicit solvent, our applications admin updated Amber14 to update.12 (and more), but when I used tleap and ran
a quick equilibration, the RNA fell apart immediately, indicating wrong parameters.
In response to the tleap command "source leaprc.ff14SB" I see the ususal libraries for RNA, a list of *12.lib files and
atomic_ions.lib and solvents.lib.
Command " set default PBradii mbondi3" response is "Using ArgH and AspGlu0 modified Bondi2 radii." There is not hint
of any nucleic acid-specific modifications. GB was run with igb=8, ntt=3, gamma_ln=1.0 and saltcon=1.0. I understand
that offset does not need to be specified (unlike in the GB-HCT protocol).
It would appear that that I am not reading the new and improved mbondi3 parameters for nucleic acids and proteins.
How should I proceed from here?
Thank you in advance, 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
http://binkley2.ncifcrf.gov/users/kasprzak
________________________________________
From: Nhai [nhai.qn.gmail.com]
Sent: Wednesday, June 29, 2016 12:07 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids
> On Jun 29, 2016, at 11:47 AM, Kasprzak, Wojciech (NIH/NCI) [C] <kasprzaw.mail.nih.gov> wrote:
>
> Hai, Carlos,
>
> Thank you again. I will pass this information to our software managers, as I am not sure
> which updates have been implemented in the Amber 14 that we have.
If you are using updated amber14, make sure you can see gb_alpha_hnu (and so on) in your mdout file.
> I'll read the paper ASAP. Is there a new tutorial for the Implicit Solvent with NA,
> or is it a matter of updated forcefield params that work better with the protocol
> I've been using (Langevin ntt=3, etc)?
>
There is no special tutorial for this since it is just matter of updating FF params like you said. You just need to specify igb=8 and use mbondi3. We have detail in the paper.
Cheer
Hai
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Received on Thu Jun 30 2016 - 12:00:02 PDT
