[AMBER] Visualisation of metal ions ligand after tleap

From: Mahendra B Thapa <thapamb.mail.uc.edu>
Date: Wed, 8 Jan 2014 15:42:02 -0500

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
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