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 - 01:30:02 PDT
