Dear David and Amber users,
Unfortunately no luck by adding the option "bymask" as follows:
trajin complex_dyn.mdcrd
center :1-95 mass origin
image origin center bymask :1-95 familiar
trajout complex_dyn.imaged.netcdf netcdf
Again the dimer splits and also the ligand separates from the dimer (as before).
Moreover in some output snapshots, the whole box translates.
Any suggestion on how to fix this issue?
Thanks!
M
2012/5/30 David A Case <case.biomaps.rutgers.edu>:
> On Wed, May 30, 2012, Massimiliano Porrini wrote:
>>
>> After having "hacked" the topology file of my system,
>> so that to have the protein (which is actually a dimer) and the ligand
>> belonging to the same solute molecule,
>> I still see them breaking up (both the two monomers and the ligand)
>> when the complex (i.e. solute) reaches the borders of the simulation box.
>>
>> I have also post-processed the trajectory centering and imaging the
>> system (the solute has 95 residues) with the following commands:
>>
>>
>> trajin complex_dyn.mdcrd
>>
>> center :1-95 mass origin
>> image origin center familiar
>
> You probably need to add the "bymask" keyword. See the example for the image
> command in the ptraj section of the AmberTools manual.
>
> ....dac
>
>
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--
Dr Massimiliano Porrini
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails : M.Porrini.ed.ac.uk
mozz76.gmail.com
maxp.iesl.forth.gr
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Received on Wed May 30 2012 - 11:30:02 PDT
