Re: [AMBER] Visualisation of metal ions ligand after tleap

From: FyD <>
Date: Thu, 09 Jan 2014 21:23:00 +0100

Dear Mahendra B Thapa,

displaying bonds between atoms depends on the file format used, and on
the distances between the atoms involved in the bonds.

when using the pdb file format in LEaP this depends on the presence of
atomic connectivities with the Cartesian coordinates in the file.

when using LEaP - if the atomic connectivities are absent you need to
use the 'bondbydistance' command to create the bonds (based on the
atomic distances; i.e. if below an internally defined threshold a bond
between two atoms is created)

when using the mol2/mol3 file format (or off file format) the bonds
reported in the file are displayed (even if above the threshold).

regards, Francois

> 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.

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Received on Thu Jan 09 2014 - 12:30:05 PST
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