Is it possible to create a script in ptraj wherein both closest and strip commands are present?
The script I used for closest:
closest 10 :200
image :WAT byres
rms first mass :1-199
The output trajectory (in order as it appears) contains :
protein
ligand
waters(10) closest
remaining tip3p water
The script was able to find the ten closest waters near the ligand (:200) and write it in the output immediately afer the protein+ligand. The problem is the unselected waters (thousands and thousands) are still in the output. I tried to experiment on adding the strip command in above script but was not successful. Also, the other way around is from the output above I make a separate ptraj script to strip the waters 211-9199. Both are not successful.
My aim is to get an output trajectory (P+L+W10), such that P=protein,L=ligand,W10=ten closest waters. And feed this into MMPBSA for binding energy calculation.
Amor
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Received on Fri Aug 20 2010 - 03:00:03 PDT
