Protein - NA complexes are difficult and need to be treated
case by case, some of them are stable others unstable whatever you
do. For a variety of reasons. Simulation problems are generally
underreported in the literature.
We made some analysis for prot-RNA systems a few years
ago but
the similar potential complitations, and there are many, are to be
expected for prot/DNA.
Problems from starting strucures may unmask on timescales far beyond 10
ns, even when using good experimental structure as the start.
https://pubs.acs.org/doi/abs/10.1021/ct5008108
Best wishes, Jiri
On Tue, 15 Feb 2022, b.ercig.nki.nl wrote:
> Date: Tue, 15 Feb 2022 23:26:29 +0000
> From: b.ercig.nki.nl
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: amber.ambermd.org
> Subject: [AMBER] DNA breaking down during the simulation
>
> Hello everyone,
>
>
>
> I am currently simulating a system which consists of 2 proteins and 1 dsDNA in complex. I have made an production run of 10ns without any problems however, when I extend the simulation after 10ns, I see that the nucleotides in DNA strand is separating from the strand for some reason. I am not sure if I was able to explain the situation. But this did not seem to be a problem with starting structure to me, since the complex structure was intact during the minimization, heating etc…
>
>
>
> I used Amber FF14SB forcefield together with BSC1 forcefield.
>
>
>
> solvateBox com TIP3PBOX 10.0 (also tried octahedral box; did not work also)
>
>
>
> and I neutralize the system using Na+; Cl- ions.
>
>
>
> Below is the parameters being used in the production run:
>
> imin=0,irest=1,ntx=5,
>
> nstlim=5000000,dt=0.002,
>
> ntc=2,ntf=2,ig=-1,
>
> cut=8.0, ntb=2, ntp=1, taup=2.0,
>
> ntpr=500, ntwx=500, ntwr = 500, ioutfm=1,
>
> ntt=3, gamma_ln=2.0,
>
> temp0=300.0,
>
>
>
> Maybe I am missing something really obvious here, and I would be really happy to hear your feedbacks. Thanks all !
>
>
>
>
>
> Kind regards,
>
> Bogac Ercig
>
> Netherlands Cancer Institute
>
>
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Received on Wed Feb 16 2022 - 00:30:03 PST
