Re: [AMBER] Antechamber prep question

From: Andrew Olson <>
Date: Thu, 9 Jul 2009 16:22:18 +0100

Here it is, taken straight from the dlg file, my starting point before adding Hs and charges.  

--- On Thu, 7/9/09, case <> wrote:

From: case <>
Subject: Re: [AMBER] Antechamber prep question
To: "AMBER Mailing List" <>
Date: Thursday, July 9, 2009, 10:16 AM

On Thu, Jul 09, 2009, Andrew Olson wrote:

> [pcp]:Research/AMBER/ATP] NAME% $AMBERHOME/bin/antechamber -i
> atp_H_1.pdb -fi pdb -o ATP.mol2 -fo mol2 -c bcc
> For atom[7]:O5, the best APS is not zero, bonds involved by this atom
> are frozen
> The frozen atom type can only be 1, 2, 3, 7 (aromatic
> single), 8 (aromatic double)Error: cannot run
> "/usr/local/Amber10/amber10/bin/bondtype -j full -i
> judgebondtype() of antechamber.c properly, exit

Can you post the atp_H_1.pdb file you use as input?  We need to be able to
reproduce the problem in order to make progress.


AMBER mailing list

Received on Thu Jul 09 2009 - 10:10:31 PDT
Custom Search