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

From: Francesco Pietra <>
Date: Thu, 8 Mar 2012 12:30:29 +0100

On Thu, Mar 8, 2012 at 12:22 PM, FyD <> wrote:
> 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.

OK. Suppose VMD has no faults (last edition). How to explain, however,
that "rdparm", through its "bonds" command, shows the bonds while
prmtop/inpcrd in VMD does not? Suppose the bonds are not correctly
defined, how to explain that "rdparm" shown them at a correct bond


>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 - 04:00:02 PST
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