Hi
On Thu, Jun 30, 2016 at 2:29 PM, Kasprzak, Wojciech (NIH/NCI) [C] <
kasprzaw.mail.nih.gov> wrote:
> 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.
Sorry, I forgot to mention that mbondi2 and mbondi3 are identical for
nucleic acid (only different for protein as you saw). So you did correctly.
> 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).
>
>
Yes, users should always use default igb=8 parameters.
Do you see below line in your mdout (to make sure you actually use updated
code)
gb_alpha_hnu = 0.53705, gb_beta_hnu = 0.36286, gb_gamma_hnu =
0.11670
If yes, how does your RNA look like?
Simulation of nucleic acid in implicit solvent is very challenging, so it
is likely that igb=8 does not do a good job here.
Hai
> 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 - 12:00:03 PDT
