Dear all,
My simulation is on a huge complex containing 6 molecules. To visualize the
trajectory and get "correct" coordinates, I usually center-n-image the
coordinates... I used to center on 1 molecule, image, and then center on 2
molecules (include the first one), and then image; and eventually center on
6 molecules and image, as suggested in some amber mailing list posts. It
worked well.
ex.
center :1-300 origin (molecule 1)
image center origin
center :1-500 origin (molecule 2)
image center origin
center :1-650 origin (molecule 3)
image center origin
center :1-950 origin (molecule 3)
image center origin
center :1-1150 origin (molecule 4)
image center origin
center :1-1300 origin (molecule 6)
image center origin
However, as the molecules deviates during the simulation, after applying
the above commands, there is always one molecule (it could be different
molecule dependent on the order I center-image on different masks...) that
just couldn't be placed back... no matter how different combinations I have
tried...
My first question is that does it make sense that the above commands work
well for first quite a few ns of trajectories but failed to wrap for the
late ns of trajectories...?
The second one will be if there is any tips or suggestions or starting
point that I could try out? I have tried different combinations, starting
center on different molecule(s), I just couldn't get all 6 back to the
correct place...
I also tried to center on reference structure...but it just put molecule
onto the geometric center, the direction is still off...I don't know how to
center molecules onto a suitable place so that all 6 could be fit into one
box...That doesn't make sense...I mean I start with an intact complex...
Thank you for any thoughts!
Best,
Guqin
--
Guqin SHI
PhD Candidate in Medicinal Chemistry and Pharmacognosy
College of Pharmacy
The Ohio State University
Columbus, OH, 43210
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Received on Sat Jul 08 2017 - 16:00:02 PDT
