> I generated a grid file for water density using ptraj using the following
> lines:
>
> trajin combine_traj.binpos
> center :1-317 mass origin
> image origin center
> rms first mass :1-317
> grid wat.dat 100 0.5 100 0.5 100 0.5 :WAT.O
>
> But when I try to view it in Chimera/VMD I am unable to do so Can anyone
> point out where the error is and how to rectify it Thank you in advance.
How are you trying to load the grid up into Chimera (or VMD)? For
Chimera, you would load this as a "CNS or XPlor density map". Of course
to view this, you need to also have a representative structure to look at
in the same frame of reference.
Additionally, macromolecules move a lot, so if you look at the average
water density around a large region (like :1-381) the density will be
smoothed by the motion so will not be so distinct or helpful.
I would suggest focusing on a particular region (or regions in separate
runs) and look at these... For example, appended is a script I've
been using to look at a DNA dodecamer with 24 residues. Note the
translate command before the "average" command which is necessary to put
the coordinates into the same frame of reference as the grid.
trajin traj.1
trajin traj.2
trajin traj.3
trajin traj.4
trajin traj.5
trajin traj.6
trajin traj.7
trajin traj.8 1 3000 1
center :1-12 mass origin
image origin center
center :1-24 mass origin
image origin center familiar
rms first mass out rms-grid :4-9,16-21
grid wat.grid 100 0.5 100 0.5 100 0.5 :WAT.O
grid na.grid 100 0.5 100 0.5 100 0.5 .Na+
grid cl.grid 100 0.5 100 0.5 100 0.5 .Cl-
translate x -0.25 y -0.25 z -0.25
average avg.pdb pdb :1-24
Then I would start up Chimera, load up avg.pdb, and before moving
anything, load up the wat.grid. Works for me.
--tec3
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 25 2010 - 09:00:04 PDT
