AMBER Archive (2009)

Subject: Re: [AMBER] Atom names

From: David A. Case (
Date: Wed Jun 03 2009 - 11:00:15 CDT

On Wed, Jun 03, 2009, Rose Tamil wrote:

> I'm trying to get parm and crd files for anthracene stacked dimer. I
> don't have any PDB for that. So i just converted my gaussian output to mol2
> using gauss view and to PDB using Babel.
> Then, i tried to get the parm and crd files using following
> commands.
> source leaprc.ff03
> loadamberparams gaff.dat
> loadamberprep PD_prep.prepin
> com=loadpdb Mol2-PDB.pdb
> saveamberparm com Mol_Final.parm Mol_Final.crd
> I'm getting some error saying that "bondAtomProblem found".

Your prepin file lists the residue name as "ANT", but the pdb file has the
residue name as "LIG". You need to edit the pdb file so that the residue name
matches the one in the prepin file.

Beyond this, the atom names in the second residue in the pdb file are all
messed up. For example, atoms C9 and C14 are supposed to be bonded to each
other, but they are 2.8 Ang. apart in the second residue (but OK in the first

It looks like you just need to rename the atoms in the PDB file to fix the


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