Dear Amber users,
Before using tleap, I did some editing (like removing connectivities of
metal ions present; keeping only A form ) of the original downloaded pdb
which binds Ca-atoms.
Naturally, I can see how Ca-atoms are connected with ligands on that
original pdb using Chimera or VMD.
I am interested to see *how the Ca-atoms are connected with ligands after
using tleap *in the pdb file which I used for minimization and production
run. I also want to check whether these connectivities change during
simulation or not.
In the 'leap.log' file, there is no information on how these Ca-atoms are
connected with ligands.
Sorry for the naive question; I went through some earlier postings but I
did not find what I exactly wanted.
Thank you for help,
Mahendra Thapa
University of Cincinnati, OH
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Received on Wed Jan 08 2014 - 13:00:02 PST
