Dear Amber users,
I've been able to implement the "closest" command in cpptraj to identify and save the water molecules that make up the first and second solvation shells around my solute. Ideally I would like to save these waters (+ solute) to a new trajectory and delete the originals, as I am low on disc space. My problem is that since I used iwrap, waters that were close to the edge of the primary unit cell are wrapped around to the other side. Presumably all the information is there to build a trajectory where this isn't the case and all the waters are in their "actual" positions with respect to the protein. Here is my current sequence of steps in ptraj:
center :1-439 origin mass
image center origin familiar :1-439
center :1-712 origin mass
image center origin familiar :1-712
center :1-861 origin mass
image center origin familiar :1-861
center :1-866 origin mass
image center origin familiar :1-866
rms first mass .C,CA,N :1-866
closest 4500 :1-866 first closestout closestmols.dat outprefix closest
The iterated rounds of centering and imaging were a suggestion I found from the archives to solve a problem with different segments of the solute being out of place. I tried preceding this sequence with "unwrap" but that did not work. Any suggestions would be greatly appreciated.
Thanks,
Andrew
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Received on Thu Dec 03 2015 - 13:30:03 PST
