AMBER: Problem while loading Pdb in xleap

From: Anju Sharma <>
Date: Wed, 21 Mar 2007 09:42:55 +0530

I removed the connect information, as well other information from the pdb
file m getting foolowing information in xleap window, when gv edit command
then only 4 atoms are visible inspite of whole structure. This much is clear
that its converting same name atoms to a single atom, bt how to undo
Hereby m enclosing the original pdb file that i hv downloaded frm net named
"original.pdb" also the pdb file i used aftr dltng connect , headers etc "

Error :
>str = loadPdb /usr/local/Anju/str.pdb
Loading PDB file: /usr/local/Anju/str.pdb
-- residue 0 : duplicate [C] atoms (total 22)
-- residue 0 : duplicate [H] atoms (total 28)
-- residue 0 : duplicate [N] atoms (total 4)
-- residue 0 : duplicate [O] atoms (total 6)

(same-name atoms are reduced to a single atom)

Unknown residue: number: 0 type: Terminal/last
.. relaxing end constraints to try for a dbase match
-- no luck
Creating new Unit for residue : sequence 0
Created new atom named : C within residue: .R< 0>
Created new atom named : N within residue: .R< 0>
Created new atom named : O within residue: .R< 0>
Created new atom named : H within residue: .R< 0>
    total atoms in file : 60
    The file contained 4 atoms not in residue templates.

Anju Sharma
Project Fellow,
NIT, Hamirpur (H.P.)

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Received on Wed Mar 21 2007 - 06:07:46 PDT
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