> 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.
...
> trajin mymdcrd
> trajout mdcrd_closest_10
> solvent byres :WAT
> closest 10 :62P oxygen noimage
You script looks fine and based on your above commentary, you are getting
output, but it "looks funny" in VMD which likely means a mismatch between
the loaded prmtop (or pdb) and the trajectory...
You need to create a compatible prmtop file, i.e. one that has the solute
(any ions if present) and *only* 10 waters so that you can view it
properly and/or process the trajectory properly. To build a prmtop with
only 10 waters can be a little tricky, but you can iteratively run a
variant of LEaP changing the buffer and/or closeness until you get only 10
waters. There is a way to generate old style prmtop's with only 10 waters
in rdparm (command: testwater) however this is not useful for newer
analysis methods in amber10/11/AmberTools.
--tec3
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 26 2010 - 10:30:05 PDT
