Thank you very much it works.
Now I have another problem I am trying to find out closest waters in my
mdcrd file but there is no output coming Can you please help me what is the
error in the input file and how to analyse these closest waters
I tried to obtain mdcrd having closest waters but when I view it in VMD the
structure looks so wierd.
Here is the input file
trajin mymdcrd
trajout mdcrd_closest_10
solvent byres :WAT
closest 10 :62P oxygen noimage
On Wed, May 26, 2010 at 12:29 AM, Thomas Cheatham III <tec3.utah.edu> wrote:
>
> > 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
>
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>
--
Hymavathi,
MS(Pharm),
Center for Pharmacoinformatics,
National Institute of Pharmaceutical Education and Research(NIPER),
Mohali,
INDIA.
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Received on Tue May 25 2010 - 11:00:03 PDT
