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 - 00:30:02 PDT
