AMBER Archive (2009)

Subject: Re: [AMBER] atom numbers

From: David A. Case (
Date: Tue Apr 21 2009 - 12:26:32 CDT

On Tue, Apr 21, 2009, Vikas Sharma wrote:

> i checked in my PDB and found out that indeed there are a few atom names
> which are same..

OK, then get a text editor out, and start fixing the PDB file. Both the
residue name (maximum 3 characters) and the atom names (max four
characters) must match between the pdb file and the mol2 file. Your
mol2 file was created by sybyl (apparently). You will need to use
antechamber to convert this to a gaff-compliant mol2 file.


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