Maybe you could use ptraj to center the solute in the box?
Bill
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 Mon Jun 11 2012 - 14:30:03 PDT
