Hi everybody,
The sequence of actions below is self explanatory:
1. strip all but closest water molecules to a given protein residue (:124) and generate a pdb file (new.pdb)
2. process a 2ns trajectory file by keeping only the closest water molecules and generate a new trajectory file (new.mdcrd)
3. create new topology files from new.pdb using tleap
The above scheme works with the following hiccup.
In step 1., the script
trajin prod_2ns.mdcrd
center :1-124 mass origin
image origin center familiar
solvent byres :WAT
closest 4 :124.N first no image
strip :Na+
trajout test.pdb pdb 1 200 1
produces 200 individual pdb files.
My questions:
Is there a way to produce only one new.pdb file? Furthermore, if the working directory contains other trajectories (e.g. prod_4ns, prod_6ns, etc.), the script scans them all - although they are not specified in the first line of the script. Any suggestions why so?
Is there a way to merge the script of step 1 with that of step 2, below?
trajin prod_2ns.mdcrd
trajout prod_closest_WAT_2.mdcrd netcdf
center :1-142 mass origin
image origin center familiar
solvent byres :WAT
closest 4 :124.N first no image
strip :Na+
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Received on Mon Jul 18 2011 - 09:30:02 PDT
