AMBER Archive (2009)

Subject: Re: [AMBER] Atom names

From: Rose Tamil (
Date: Wed Jun 03 2009 - 09:53:51 CDT

Hi all,
        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

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". I don't know how
to fix it. I've attached my output file, PDB and prep file. Could you please
help me to fix this problem?
Thanks in advance.

On Tue, Jun 2, 2009 at 12:50 PM, Rose Tamil <>wrote:

> Thanks to Carlos Simmerling and David for your reply. I got that PDB by
> writing gaussian output file as PDB in molden. When i viewed in molden, it
> looked alright. I didn't view it in VMD. I'll try to fix that problem.
> Thanks again.
> On Tue, Jun 2, 2009 at 12:44 PM, David A. Case <>wrote:
>> On Tue, Jun 02, 2009, Rose Tamil wrote:
>> > com=loadpdb PD_PDB.pdb
>> The file "PD_PDB.pdb" has garbled coordinates that look nothing like an
>> anthracene dimer. You will need to fix this, since this is where LEaP
>> gets
>> the coordinates.
>> ...dac
>> _______________________________________________
>> AMBER mailing list

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