AMBER Archive (2009)

Subject: Re: [AMBER] atom numbers

From: Vikas Sharma (
Date: Tue Apr 21 2009 - 12:15:07 CDT

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 <>
To: AMBER Mailing List <>
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.


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