Re: [AMBER] Problem with molegro file

From: FyD <>
Date: Sun, 29 Apr 2012 09:16:39 +0200

Dear Chris,

> I have an organic molecule (coelenterazine) that was generated in
> the molegro molecular viewer and then exported as a pdb. I want to
> put it into antechamber for processing so I can use in AMBER. The
> problem is that the pdb file looks like it has too many bonds to
> each atom. Can anyone tell me how to fix this problem.

When using the PDB file format some graphical programs (vmd...)
automatically display an atom connectivity when the distance between 2
atoms is below a threshold internally stored.
Others (LEaP) do display the bonds only when requested by the user
(use of the 'bondbydistance' command), or when the CONECT keywords are

If I use your PDB file & try to display it in VMD or in LEaP after
having executed the 'bondbydistance' command too many bonds are
generated; this means your PDB file has a problem of format or is not
well constructed...

If you look in wikipedia, you can get the SMILES, from the SMILES you
can convert it into a PDB file (at; from this PDB file I generated
a P2N file using R.E.D. Server/Ante_R.E.D. and from R.E.D.
Server/R.E.D. IV I generated the mol2 file you will need...
P2N file:
mol2 file:

regards, Francois

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Received on Sun Apr 29 2012 - 00:30:03 PDT
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