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

From: Hai Nguyen <>
Date: Mon, 23 Jul 2018 14:06:32 -0400


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).


On Sun, Jul 22, 2018 at 2:30 PM, Supriyo Bhattacharya <>

> 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
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Received on Mon Jul 23 2018 - 11:30:02 PDT
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