Re: [AMBER] Viewing with VMD bonds set by the "bond" command

From: FyD <>
Date: Thu, 08 Mar 2012 12:22:40 +0100

Dear Lorenzo, Francesco,

> I suppose that VMD displays a bond (or not) on the basis of an
> internal cutoff (how long are your bonds?).
> But maybe I am wrong. In the newest version (1.9) you can also
> explicitly link two atoms, or you can use the topotools plugin ("topo"
> command in the VMD shell) to generate a topology.

if you load two prmtop/prmcrd files (or a mol2 file) into VMD a bond
(if it is correctly defined) should be displayed independently of its
length. I do not think there is a threshold here. This can be easily
tested using a model with a very long S-S disulfide bridge between two
CYX residues for instance...

if you load a PDB file without any atom connectivity into VMD a bond
should be displayed ONLY below an internal threshold; Yes.

if you load a PDB file with an connectivity for a very long bond: to
be tested ;-)

regards, Francois

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Received on Thu Mar 08 2012 - 03:30:04 PST
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