Thanks for the tip. I ran the ash pdb using my same command line and it
does look better ('c' and 'c3' now which makes more sense at least.) The
text from my input pdb is below although I'm busy looking into new tools
thanks to heads up from Dean.
Thank you for both for the quick responses,
-denny-
//benzene saved out from avogadro
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 C LIG 1 -2.325 2.192 -0.017 1.00 0.00
C
HETATM 2 C LIG 1 -2.355 0.797 -0.009 1.00 0.00
C
HETATM 3 C LIG 1 -1.162 0.074 0.005 1.00 0.00
C
HETATM 4 C LIG 1 0.060 0.746 0.010 1.00 0.00
C
HETATM 5 C LIG 1 0.090 2.141 0.002 1.00 0.00
C
HETATM 6 C LIG 1 -1.103 2.863 -0.012 1.00 0.00
C
HETATM 7 H LIG 1 -3.255 2.755 -0.028 1.00 0.00
H
HETATM 8 H LIG 1 -3.307 0.274 -0.013 1.00 0.00
H
HETATM 9 H LIG 1 -1.185 -1.012 0.012 1.00 0.00
H
HETATM 10 H LIG 1 0.990 0.183 0.021 1.00 0.00
H
HETATM 11 H LIG 1 1.042 2.664 0.006 1.00 0.00
H
HETATM 12 H LIG 1 -1.080 3.950 -0.019 1.00 0.00
H
CONECT 1 2 2 6 7
CONECT 2 1 1 3 8
CONECT 3 2 4 4 9
CONECT 4 3 3 5 10
CONECT 5 4 6 6 11
CONECT 6 5 5 1 12
CONECT 7 1
CONECT 8 2
CONECT 9 3
CONECT 10 4
CONECT 11 5
CONECT 12 6
MASTER 0 0 0 0 0 0 0 0 12 0 12 0
END
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
Of case
Sent: Friday, March 12, 2010 4:47 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Antechamber question: all my residue carbons are the
same 'c3' atom type.
On Thu, Mar 11, 2010, Denny Bromley wrote:
>
> My amino acid PDB files were from the Avogadro fragment library and
exported
> via Avogadro into the PDB format.
It would help if you could post one of the input pdb files. You could
look at the test case in $AMBERHOME/test/antechamber/ash, where an aspartic
acid molecule is handled, and not all carbon atoms are c3. Try to figure
out
what is different from your input and that one. A similar example is in
the ../guanine_amber directory. [I'm assuming all the test cases pass, or
you
would have said something.]
....dac
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Received on Fri Mar 12 2010 - 10:00:03 PST
