Hi,
Can you be more specific about what issues you encountered when trying
to use 'autoimage' to re-image your DNA? Were there any warnings or
errors? What version of cpptraj was used?
I'm always looking to improve the 'autoimage' action; I'd like to fix
any issues present. Thanks!
-Dan
On Wed, Dec 2, 2020 at 5:05 AM lomzov <lomzov.niboch.nsc.ru> wrote:
>
> Hi,
>
> We were not successful to unwrap DNA duplexes using cpptraj.
>
>
> To solve this problem at the modeling stage, we found two solutions:
> 1) as suggested by Anselm using iwrap = 0, but for long-term simulations
> (more than 50-100 ns) water molecules and cations may go too far and
> this cannot be written to the old format mdcrd file.
> To solve this issue you can simulate with iwrap = 0 for 50 ns, and than
> short simulate iwrap = 1 for 5-10 ns.
> Sometimes it helps.
>
> 2) use very weak Cartesian restraints (0.01 kcal / mol / A) for two
> atoms in opposite chains with iwrap = 1. For example, for 16 bp duplex
>
> ntr = 1,
> restraint_wt=0.01 ,
> restraintmask=" :8,24.C4'",
>
> This does not allow translation movement of the duplex, but becaose of
> low value of restraint does not change duplex conformation.
> If you want to analyze conformation changes, you could restart
> simulation every few nanoseconds (5-10 ns) using the reference file,
> which was obtained at previous stage
>
> stage 1: ..... -r 1.restrt -ref 0.inpcrs
> stage 2: ..... -r 2.restrt -ref 1.restrt
> stage 3: ..... -r 3.restrt -ref 2.restrt
>
>
> good luck!
>
> Alex
>
>
> On 02.12.2020 16:23, Dr. Anselm Horn wrote:
> > Hi,
> >
> > just to add a comment:
> > If you used iwrap=1 in your simulation input, try to use the unwrap
> > command in cpptraj, expecially, if you are not interested in the solvent
> > molecules: strip off these first, the do the unwrap and omit the
> > (auto)image commands.
> >
> > However, you may want to use a rms fit command to obtain a trajectory
> > better to visualize.
> >
> > Regards,
> >
> > Anselm
> >
> >
> > On 12/02/2020 09:12 AM, Gustaf Olsson wrote:
> >> Short of increasing the solvent buffer to avoid jumps, trying to play around with the masks for image/autoimage seems reasonable.
> >>
> >> See what happens if you autoimage with a mask defined. Either trying to center the entire DNA or as suggested (https://amberhub.chpc.utah.edu/autoimage/), try imaging using a small region of the DNA which should be close to the center of the box.
> >>
> >> Best regards
> >> // Gustaf
> >>
> >>
> >> On 2 Dec 2020, at 08:17, Satyaseelan C <bo17resch11006.iith.ac.in<mailto:bo17resch11006.iith.ac.in>> wrote:
> >>
> >> Dear Amber users,
> >> I am facing an imaging issue during the MD simulation of a
> >> DNA duplex. Due to this, the RMSD is shooting up and falls back during the
> >> middle of the simulation. I am observing this problem for 50ns during the
> >> simulation. I used autoimage option followed by image option as below:
> >>
> >> parm prmtop
> >> trajin trajin.nc
> >> autoimage
> >> center :1-16 origin
> >> image origin center familiar
> >> center :1-32 origin
> >> image origin center familiar
> >> trajout reimage.nc
> >> go
> >>
> >> When I don't apply any imaging, the DNA strands are separated and going out
> >> of the box in some frames. But, after performing imaging, the problem is
> >> not completely resolved. Here, a stretch of DNA strand is going away and
> >> causes distortions in the structure for 50ns. I have attached the
> >> corresponding snapshots.
> >>
> >> Please suggest any alternative options to overcome this issue.
> >>
> >>
> >> Thanks in advance
> >> Sathyaseelan
> >>
> >> --
> >> *Thanks & Regards*
> >>
> >> *C .Sathyaseelan *
> >> *PhD Research Scholar*
> >> *C/o Dr. Thenmalarchelvi Rathinavelan*
> >> *Molecular Biophysics Lab*
> >> *Dept. of Biotechnology*
> >> *Indian Institute of Technology (IIT)*
> >> *Kandi, Hyderabad, Telangana - 502285*
> >> *Ph.No 6383836804, 8300150807*
> >>
> >> --
> >>
> >>
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Received on Fri Dec 04 2020 - 12:30:02 PST
