Hi Oliver,
This isn't a COM translation problem. Keep in mind that a simulation has no
idea of the distinction between solvent and solute when it comes to
determining center of mass, so while dan was right and ncsm performs as he
described, that will not prevent your complex from splitting apart.
The reason this is actually happening is due to your use of iwrap. One
monomer is getting wrapped to the other side of the periodic box when it
comes too close to the edge of the box. The solution in my experience is to
center and image once for each individual species that is in your system.
In the case of a non-bonded dimer with a ligand, that is 3x. The first is
the first monomer, the second is both monomers, and the 3rd is both monomers
and the ligand. This should put everything back into the same box (and you
might as well strip waters and ions and use "strip_mdcrd=0" in your
MMPBSA.py input file).
Hope this helps,
Jason
On Mon, Jul 19, 2010 at 9:55 AM, Oliver Kuhn <oak.amber.web.de> wrote:
> Thanks Dan,
> I'm very much worried about that being the only solutions because I have
> already dozens of 4-10ns simulations on which I want to do binding affinity
> calculations.
> I hope that it is also possible to transform these trajectories into such
> that can be used as input for MMPBSA.
>
>
> >Oliver,
> > Is it a problem with the COM motion? If so, you can simply set the
> nscm=10
> >(default 1000)
> >or some other small number (much smaller than your COM diffusion rate I
> >would guess).
> >This will reset the center of mass to the origin every nscm steps.
> >I think this corresponds to your possibility #1. To me this is the easiest
> >solution.
> >--Dan
> >
> >On Mon, Jul 19, 2010 at 9:04 PM, Oliver Kuhn <oak.amber.web.de> wrote:
> >
> >> Dear Amber Users and Developers,
> >> I'm still having trouble with a well know issue: A dimeric protein
> diffuses
> >> across the periodic boundary and is split into monomers (as can be seen
> in
> >> the attached png).
> >> The trajectory is needed for a MMPBSA.py calculation.
> >>
> >> I know several possibilities to circumvent this issue in principle but
> none
> >> works.
> >>
> >> 1. The center-of-mass motion should be removed by default so that the
> >> protein stays in the box center - please correct me if I'm wrong.
> >> (Or do I have to remove comm more often than default?)
> >>
> >> 2. iwrap=1 should map all atoms into the primary box when writing the
> >> trajectory.
> >>
> >> 3. tleap can be used to map the atoms back into the primary box - this
> is
> >> somewhat tricky (by centering two times - on time without and then with
> >> ligand) implemented in the MMPBSA.py script:
> >> trajin production.mdcrd 1 1000 1
> >> strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
> >> center :1-198 mass origin
> >> image origin center
> >> center :1-199 mass origin
> >> image origin center
> >> rms first mass :1-198
> >> average _MMPBSA_avgcomplex.pdb pdb
> >> trajout _MMPBSA_complex.mdcrd nobox
> >>
> >> In the end, I still run into problems with my energy calculations (as
> can
> >> be seen in the attached pdf - 20 simulations with 3 of them having PBC
> >> effects).
> >> Can anybody tell me how to prepare the trajectories so that monomer1,
> >> monomer2 and ligand coordinates are in one box?
> >>
> >> Thanks for any help
> >> Oliver
> >--
> >Dr. Daniel J. Sindhikara
> >Institute for Molecular Science
> >E-mail: sindhikara.gmail.com
> >Website: http://sites.google.com/site/dansindhikara/
> >--
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Jul 19 2010 - 08:30:03 PDT
