Hi,
What version of cpptraj are you using? I recently fixed an issue that
could impact imaging in cases where there is non-contiguous atom
ordering. You may want to try the latest version of cpptraj and see if
'autoimage' works.
Otherwise feel free to send me your topology and coordinates off list
so I can try to reproduce your issue.
-Dan
On Wed, Apr 6, 2022 at 4:07 AM Sathyaseelan C <bo17resch11006.iith.ac.in> wrote:
>
> Dear Amber users,
>
>
>
> I am facing an imaging issue during the MD simulation of a
> DNA duplex with trivalent cations. The maging issue happens throughout the
> simulation due to the terminal dimer of one of the DNA strands as well as
> some of the trivalent ions. For instance, in one step the DNA dimer is out
> of the box (as a fragment), but, in the next step it comes back to the
> periodic box and becomes part of the duplex. This happens throughout the
> simulation. I tried with imaging options as below, but, were not useful.
> Any suggestion is highly appreciated.
>
>
>
>
> *For RMSD*
>
>
>
> *1) **Using Image option*
>
> parm prmtop
>
> trajin trajin.nc
>
> reference ../../input/prmcrd
>
> center origin :1-32 # DNA residues
>
> image origin center
>
> center origin :33-44 # trivalent cations
>
> image origin center
>
> strip :WAT
>
> strip :LA
>
> strip :CL
>
> trajout test.pdb pdb
>
> go
>
>
>
> *2) **Using Autoimage option*
>
>
>
> parm prmtop
>
> trajin trajin.nc
>
> reference ../../input/prmcrd
>
> autoimage
>
> strip :WAT
>
> strip :LA
>
> strip :CL
>
> trajout test.pdb pdb
>
> go
>
>
>
>
>
>
>
> 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 Apr 06 2022 - 07:00:03 PDT
