> That is a good suggestion, however also the cloud of counterions
> should accompany the protein-complex. Don't know how to do that.
It shouldn't matter. Relative position to solute should remain
the same.
Bill
Francesco Pietra <chiendarret.gmail.com> wrote:
> On Mon, Jun 11, 2012 at 11:08 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > Maybe you could use ptraj to center the solute in the box?
> >
> > Bill
>
> That is a good suggestion, however also the cloud of counterions
> should accompany the protein-complex. Don't know how to do that.
> Actually, MD is going on without any problem: protein-complex and
> counterions remain inside the water box, albeit not at the center. I
> assume that there should be nothing wrong in continuing this way (I
> would like to see if the ligand adapts to the enzyme active center; so
> far it is going this way).
>
> thanks
> francesco pietra
> >
> > Francesco Pietra <chiendarret.gmail.com> wrote:
> >
> >> Hi:
> >>
> >> Having solved (thanks to addIonsRand) the problem of setting
> >> homogeneously a high number of single-charge ions around the protein
> >> in a water box, I am now trying to have the protein placed with its
> >> center of mass at the center of the box, which was not the case with
> >> ambertools12 LEaP.
> >>
> >> I wonder whether there is a way to intervene manually on the prmtop
> >> file. I am only aware about
> >>
> >> %FLAG BOX_DIMENSIONS
> >> %FORMAT(5E16.8) OLDBETA, BOX(1), BOX(2), BOX(3)
> >> OLDBETA : periodic box, angle between the XY and YZ planes in
> >> degrees. This is now redundant, as it is present in the
> >> inpcrd files. It is ignored here.
> >> BOX : the periodic box lengths in the X, Y, and Z directions.
> >> This is now redundant, as it is present in the inpcrd files.
> >> It is ignored here.
> >>
> >> The following are only present if IFCAP .gt. 0
> >>
> >> %FLAG CAP_INFO
> >> %FORMAT(10I8) NATCAP
> >> NATCAP : last atom before the start of the cap of waters
> >> placed by edit
> >>
> >> %FLAG CAP_INFO2
> >> %FORMAT(5E16.8) CUTCAP, XCAP, YCAP, ZCAP
> >> CUTCAP : the distance from the center of the cap to the outside
> >> XCAP : X coordinate for the center of the cap
> >> YCAP : Y coordinate for the center of the cap
> >> ZCAP : Z coordinate for the center of the cap
> >>
> >> The "5E16.8" section is indeed present in my prmtop file, however
> >> clearly not manageable. Is any raw information about the center of
> >> mass of the protein relatively to the center of the box, on which to
> >> intervene?
> >>
> >> What is wrong in my pdb fine, so that the result of "5E16.8" is
> >> misplacing the protein into the water box, defeated my understanding.
> >>
> >> Thanks
> >> francesco pietra
> >>
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Received on Tue Jun 12 2012 - 16:00:02 PDT
