Dear Bogac,
To me it sounds like this is not an imaging issue but rather bases
flipping outwards if I understand it correctly. Does this happen close
to the protein or in a region of DNA without protein contacts ? I also
assume you do not talk about terminal bases either.
We always use basepair restraints (the WC hbonds) as well as restraints
of the well established protein-DNA contacts during large portions of
the equilibration to make sure the DNA does not get distorted in any way
and the protein-DNA interface relaxes well before letting everything
free. This usually worked well for the systems we studied so far ....
We have seen something similar when we modified DNA bases to study
alternative DNA binding site sequences and did not use any restraints
during equilibration ... But I assume you did not modify the sequence of
your DNA ...
Did you also checked carefully the conformation of the nucleotide in
your starting structure ? We've seen that as well in structures,
nucleotides flipped with distorted WC base pairing ....
I am happy to help if you want to share with me an example stucture off
the list ..
Cheers
Vlad
On 2/16/22 00:26, b.ercig.nki.nl wrote:
> 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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--
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Wed Feb 16 2022 - 01:00:02 PST
