On Thu, Jun 30, 2016 at 3:09 PM, Kasprzak, Wojciech (NIH/NCI) [C] <
kasprzaw.mail.nih.gov> wrote:
> Hai,
>
> I am trying to compare the GB-neck2 protocol to the GB-HCT (for which I
> see decent, but
> not perfect results, as would be expected). Based on your 2015 paper, the
> results should
> improve with the new mbondi3/igb=8. The fact that my RNA nanocube begins
> to fall apart
> in minimization and does not even look like RNA after a few equilibration
> steps makes me
> suspicious about the parameters read-into leap and/or binary I am using.
>
>
> I do not see any of the gb_alpha_hnu = 0.53705, gb_beta_hnu =
> 0.36286,
> gb_gamma_hnu = 0.11670 in the output file, but it is not clear to me if
> things failed in leap or
> are ignored in pmemd.cuda.
>
This indicates that you did not use updated igb8 parameters for nucleic.
Please tell your admin to recompile AMBER after applying updates.
> Is there something I could check in the prmtop or inpcrd files created in
> tleap to isolate the issue
> better?
>
No, there is no special thing about tleap with igb8, except that you need
to use mbondi3.
You can use vim to open your prmtop and search for mbondi3 keyword. If you
found it, it's good to go.
But please recompile AMBER code and
make sure you DO see gb_alpha_hnu, gb_beta_hnu, ... nucleic acid parameters
in your mdout.
Hai
>
> Thank you, Voytek
>
> 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: Hai Nguyen [nhai.qn.gmail.com]
> Sent: Thursday, June 30, 2016 2:48 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] GB-neck2 MD with nucleic acids
>
> 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
>
>
>
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>
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Received on Thu Jun 30 2016 - 12:30:04 PDT
