if u see the Mol2 file of the ligand and the protein-ligand complex pdb, u'll see that two carbons and 4 oxygens are named as C,C and O,O,O,O respectively...they have same names
________________________________
________________________________
From: David A. Case <case.biomaps.rutgers.edu>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Tuesday, 21 April, 2009 9:22:22 PM
Subject: Re: [AMBER] atom numbers
> "source leaprc.ff03
> source leaprc.gaff
> com = loadpdb 'prot-ligand complex.pdb'
>
> it gave the result as:
>
> residue 317:duplicate [c] atoms (total 2)
> residue 317:duplicate [o] atoms (total 4)
> warning: atom names in each residue should be unique.
> (same-name atom are handled by using the first
> occut=rence and by ignoring the rest.
You have to fix this in the pdb file: atom *names* (not numbers!) in
each residue must be unique.
> Unknown residue: M_$ no:221 type:terminal/last
> Creating a new unit for residue : M_4 sequence:317
> Created a new atom name:C in residue:.R<M_4 317>
Your pdb file has a residue named "M_4", but LEaP has no idea what this
means. See tutorial B4 for an introduction on how to handle
non-standard residues.
....dac
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Received on Wed May 20 2009 - 12:08:22 PDT
