Re: AMBER: Problem while loading Pdb in xleap

From: Sandeep Kaushik <>
Date: Thu, 22 Mar 2007 15:37:13 +0530

Hi Anju,
Any unit that is loaded in LEaP cannot have atoms with same name.. for
example in ur case LEaP will take the molecule as a single unit as there is
no description about the residues this molecule is composed of.. that place
is left blank..... only atoms have been given..

So either you can specifiy the residues that you see in ur molecule and in
ur force field as well and then name the atoms according to the residues
found in the force field... OR
you can name the atoms differently like C01, C02, C03 etc, assign the
atomtypes and charges to the atoms (acc to the FF), and make a new unit,
save it as an OFF file (X.lib).
Once you do that load ur FF, then load ur X.lib, and finally load ur
I think it should be enough to get it loaded properly..
And like mentioned in the manual ......keep ur eyes open for any error and
try untill you don't get one.......


On 3/21/07, Anju Sharma <> wrote:
> 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
> this....
> 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 "str.pdb"
> 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 Sun Mar 25 2007 - 06:07:24 PDT
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