Carlos, Hai,
I believe things are getting sorted out on our side. A clean login to the server and fresh initializations of all paths
got the right binary running. I do see the mbondi3 section in the prmtop file now, and I do see the output
containing b_alpha_hnu, gb_beta_hnu, etc. (The updates were installed in a temporary area, in parallel with
the "production" binaries, hence some confusion). The product of minimization also looks clean.
The equilibration steps are under way now. Thank you very much for immediate help and hand-holding!
Regarding equilibration protocol, ours looks like the one described in your paper, with gradually diminishing
restraints going down to 0.1 kcal/mol/A^2 before un-restrained MD begins, but I am curious if
you are using and/or recommending varying gamma_ln (for the ntt=3) at various stages of it. What
setting do you use? Also, is gbsa option any more important to GB-neck2 than before? Setting gbsa=1 slows
down my runs dramatically while the listed values are very small. My current test run is with gbsa=0.
To clarify my past e-mails, I am dealing with DNA and RNA nanocubes. In GB-HCT DNA cubes looked more
stable than the RNA cubes, and I am trying to see if GB-neck2 can improve the results. Both are quite stable
in explicit solvent simulations (PME, TIP3P)
Thank you very much again!
Best regards, 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: Hai Nguyen [nhai.qn.gmail.com]
Sent: Thursday, June 30, 2016 3:23 PM
To: AMBER Mailing List
Subject: Re: [AMBER] GB-neck2 MD with nucleic acids
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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jun 30 2016 - 13:30:02 PDT
