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 Wed Dec 02 2020 - 02:30:02 PST
