Thanks Jason,
Actually I had already tried to center the solute unit by unit like this
(and you almost guessed well the units decomposition of my solute ;-) ):
trajin complex_dyn.mdcrd
center :1-14 mass origin
image origin center familiar
center :1-54 mass origin
image origin center familiar
center :1-95 mass origin
image origin center familiar
trajout complex_dyn.imaged.netcdf netcdf
But no luck even with this centering/re-imaging.
As Thomas pointed out (and I must agree) there is a problem
in generating the trajectory, in that if my units belong to the same molecule
(i. e. solute) they are not supposed to separate during the wrapping;
given that I have properly
"hacked" the topology file.
And, in doing this, I have simply followed a "recipe" posted by
Carlos Simmerling a while ago in this mailing list.
By the way, I am going to send Thomas my files off list and let's see
if we can get this issue sorted out.
Thanks again.
Max
2012/5/30 Jason Swails <jason.swails.gmail.com>:
> 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
> _______________________________________________
> 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
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Received on Thu May 31 2012 - 05:00:04 PDT
