Hi,
On Fri, May 4, 2012 at 5:39 AM, Thomas Cheatham <tec3.utah.edu> wrote:
> The key is how you view with VMD. You cannot load the original prmtop
> file since this will have all the waters; there is no information in the
> trajectory file to specify what atom is what, only a list of x, y, z for
> atoms 1->N. Therefore you need some way to map and this requires either
> loading a corresponding PDB file (with no ions and only 10 waters) or a
> corresponding prmtop file (with no ions and only 10 waters).
Note that AT12 cpptraj can now generate a matching prmtop for you automatically:
trajin md_reimaged.mdcrd 201 400
trajout closest_waters.mdcrd
strip :Na+
closest 10 :13 oxygen outprefix strip
This will create a prmtop that matches the output from 'closest'
called strip.<parmname> where <parmname> is your original parm
filename. If you use cpptraj though make sure the latest bugfixes are
applied since AT12 bugfix 5 applies to cpptraj 'closest'.
-Dan
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Received on Fri May 04 2012 - 04:00:05 PDT
