Re: Re: unwanted bonds in .pdb file while using molefacture

From: Josť (
Date: Wed Aug 06 2008 - 15:40:45 CDT

Hello Subhashis,

What you are seeing is because the molecule viewer detects atoms in a
short separation and automatically connects those atoms. You can avoid
this by setting a different phi and psi for your residues other than the
default values 0 or 180, so the atoms are apart by more than the
covalent bond distance. In the molefacture you may set the phi and psi
angles before adding the new residue to the sequence.

hope it helps,


Subhashis Biswas escreveu:
> Hi,
> I have developed a peptide sequence using molefacture, and saved it as
> .pdb. Then while I am opening it from the VMD main window as file/new
> molecule, it is showing me some unwanted bonds between close atoms and
> forming a crumbled type structure.
> I have attached the file here. If someone can take a look and suggest
> how to get rid of those bonds , will be really of great help.
> Thanks
> regards,
> Subhashis

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