AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber prep question

From: Andrew Olson (
Date: Thu Jul 09 2009 - 12:00:19 CDT

I get the same error after adding hydrogens(attached);
[pcp:Research/AMBER/ATP] NAME% $AMBERHOME/bin/antechamber -i atp_H_1.pdb -fi pdb -o atp_H_1.mol2 -fo mol2 -c bcc
For atom[13]: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 ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit
any thoughts
--- On Thu, 7/9/09, case <> wrote:

From: case <>
Subject: Re: [AMBER] Antechamber prep question
To: "AMBER Mailing List" <>
Date: Thursday, July 9, 2009, 11:48 AM

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

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

You have to add the hydrogens (not the charges) *before* sending the file to
antechamber.  (sleap can automatically add hydrogens, but it is usually safer
to do it manually, especially for a charged ion.)  Your file has hydrogens on
polar atoms, but is missing the hydrogens on the carbon atoms.


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