Re: [AMBER] Antechamber prep question

From: Andrew Olson <muchemfu.yahoo.com>
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 <case.biomaps.rutgers.edu> wrote:

From: case <case.biomaps.rutgers.edu>
Subject: Re: [AMBER] Antechamber prep question
To: "AMBER Mailing List" <amber.ambermd.org>
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
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> 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.

...thx...dac


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