Re: [AMBER] Question about implicit solvation: DNA-linker conjugate

From: Supriyo Bhattacharya <>
Date: Wed, 25 Jul 2018 17:32:20 +0000 (UTC)

 Dear Matias,Thank you for pointing me to parmed. I am going to check it out. Right now, I assigned the new residue one of the recognized nucleotide residue names. This allows Amber to recognize it as a nucleotide and assign the nucleotide GB parameters. This seems to have solved the problem for now, but I understand that it's an unclean solution. So, the proper way would be to provide the right parameters in the topology itself.
As for suggesting the salt concentration, that was really helpful. This was not a problem for the protein simulations, but with DNA, setting the saltcon to 0.15 solved the issue of DNA unfolding. Now, the DNA structure is completely stable for 1 microsec and counting.
Thanks so much for both the suggestions. You guys are a wonderful community!

    On Tuesday, July 24, 2018, 7:44:06 AM PDT, Matias Machado <> wrote:
 Dear Supriyo,

You can modify the GB parameters in the topology with Parmed using the command "change RADII <mask> <new-value>" (check de manual)...

By the way, are you setting the an ionic concentration while running with GBSA (e.g. saltcon=0.15)? That may be very important to avoid polyelectrolite melting as they are heavy charged molecules...



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "Supriyo Bhattacharya" <>
Para: "AMBER Mailing List" <>
Enviados: Lunes, 23 de Julio 2018 17:53:50
Asunto: Re: [AMBER] Question about implicit solvation: DNA-linker conjugate

 Hello Dr. Simmerling,Thank you for the reply. I would like to carefully assign the GB parameters myself, but I am looking for a way to provide the parameters in the leap input file or the run script without having to edit the source code. Is there a way to do this?
Many thanks,Supriyo

    On Monday, July 23, 2018, 11:11:47 AM PDT, Carlos Simmerling <> wrote: 
 Gb neck was only tested with proteins and nucleic acids, and the intrinsic
Born radii are optimized for those. If you create a new molecule (such as
your linker), you'll also want to carefully check the radii that leap
assigns to those atoms. They may not be appropriate. You'll probably want
to try to assign them by analogy rather than the guess leap takes.

On Mon, Jul 23, 2018, 2:06 PM Hai Nguyen <> wrote:

> hi,
> which amber version you're using? (Just to make sure you have updated igb8
> parameters for DNA/RNA in amber 17 or 18).
> By the way, 310K is pretty high in GB simulation (in my experience), you
> can try with 300K.
> >  The same system when simulated in explicit water remains stable and does
> not show aggregation of the phosphates.
> How long did you run? (implicit solvent has faster sampling, so you might
> want to run much longer explicit water to compare).
> Hai
> On Sun, Jul 22, 2018 at 2:30 PM, Supriyo Bhattacharya <>
> wrote:
> > Hi everyone,I am trying to simulate the dynamics of a linker conjugated
> > DNA strand using implicit solvation in AMBER. The formula of the
> molecule I
> > am trying to simulate is:
> >                                                                |    |  |
> >  |  |  |  |  |  |    |  |  |  |  |  |      |
> >
>  3'-L-L-L-L-G-T-A-A-A-G-G-G-C-A-T-T-T-A-G-L-L
> > , where L (linker) = -(PO4)-(CH2)-(CH2)-(CH2)-
> > I have parameterized the linker using Antechamber and assigned am-bcc1
> > charges. Next I edited the linker prepi file in xleap and specified the
> > head and tail atoms. Finally, I created a frcmod file where I specified
> the
> > missing parameters (mostly the connections between L and nucleotides)
> taken
> > from the DNA.bsc1 parameter set. When I performed a test run using igb=8
> at
> > 310K, all the phosphate groups in the linker aggregated together
> > immediately and destroyed the DNA double helix. The same system when
> > simulated in explicit water remains stable and does not show aggregation
> of
> > the phosphates.
> > Could someone with experience advise what is going wrong with the
> implicit
> > solvation. Do I need to set any other parameter for the linker phosphates
> > specific to GB solvation (explicit water simulations work fine). Also,
> the
> > partial charges on the phosphate group are similar if not identical to
> the
> > DNA phosphates. The missing dihedral parameters for the linker were also
> > taken from equivalent parameters in DNA. I am wondering whether the
> alpha,
> > beta and gamma parameters of IGB need to be explicitly set for the linker
> > atoms. I thought some default reasonable values are already assigned by
> > AMBER. Please note, I have some prior experience with GB solvent
> > simulations in AMBER, although all of them were with pure protein
> systems.
> > Could somebody help?
> > Many thanks in advance,Supriyo
> > _______________________________________________
> > AMBER mailing list
> >
> >
> >
> _______________________________________________
> AMBER mailing list
AMBER mailing list
AMBER mailing list

AMBER mailing list
AMBER mailing list
Received on Wed Jul 25 2018 - 11:00:02 PDT
Custom Search