You mentioned that you have a dimer with a ligand, and your ptraj script
suggests you have 95 solute residues, or 1 ligand residue and 2 monomers
each with 47 residues. My suggestion will assume the above (although it
can be adjusted in a rather straightforward way).
First, modifying the prmtop is potentially hazardous. ParmEd allows you to
combine molecules, and I would suggest using that to 'hack' the prmtop
rather than doing it by hand, since it eliminates mistakes.
To the ptraj imaging. If your solute molecules get imaged separately, then
the command
center :1-95 mass origin
will in all likelihood not bring them back together. The reason is that
they are on either side of the box, so the center of mass will not likely
change. What you should do is center only the first molecule and image
everything around that center. That should bring all of the solute
molecules back into the same box. Then, center and image again around your
whole solute to bring the COM of the properly imaged solute as the center
of the box. So your ptraj script will look something like this:
center :1-47 mass origin
image origin center familiar
center :1-95 mass origin
image origin center familiar
HTH,
Jason
P.S. If your ligand still seems split away from the rest, you may need to
break it up into 3 steps -- center and image around the first monomer, then
around the dimer, then around the whole complex.
On Wed, May 30, 2012 at 11:05 AM, Massimiliano Porrini
<M.Porrini.ed.ac.uk>wrote:
> 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed May 30 2012 - 15:30:03 PDT
