AMBER Archive (2009)

Subject: [AMBER] non standard residue and bond command

From: Neha Bharat Gajaria (n.gandhiau_at_gmail.com)
Date: Wed Dec 16 2009 - 03:50:02 CST

Hi List,

I have a big molecule which I cannot run directly using antechamber.
So I split the residues into 4 parts HE1, HE2, HE3 and HE4
respectively and convert them to prepi files as well as change the
residue name accordingly in PDB file. I used TER between each residue
in pdb file to avoid the warnings for long distance between two atoms
as per suggestions in amber archives.

I load the prepi files first, then the pdb file. I try to use bond
command and try to connect with single bond between two residues e.g.
HE1.O60 and HE2.C39 Now as the residues are from two different units,
the bond command doesnt create a single bond, there are no errors or
warnings but I simply dont see a bond between two residues when I try
to save a new pdb file.

What should I do to create bond between residues HE1 and HE2 and others as well.

Thanks 

-- 
Regards,
Neha Gandhi Gajaria,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845

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