[Chimera-users] error running Antechamber

Elaine Meng meng at cgl.ucsf.edu
Fri Jun 22 12:34:40 PDT 2007

Hi SD,
As I understand it, Antechamber is not meant to be used on metal 
complexes or on inorganic compounds. Trying to use it for such 
structures may give failures (as in your case) or unreasonable results.

Here is some text from the Antechamber website ( 
http://amber.scripps.edu/antechamber/tips.html ):

"Bondtype works for most of organic molecules that are made of C, N, O, 
S, P, H, F, Cl, Br, I. It may not work well for high-charged molecules 
and molecules with too many unusual valence states."

Bondtype is a routine in Antechamber; I believe the other routines have 
similar restrictions.

For structures not handled by Antechamber, it is necessary to use some 
other, outside program to calculate partial charges, or to find them in 
the literature.  The charges can then be loaded into Chimera using 
Define Attribute (or the command "defattr") or by reading in a *.mol2 
file with charges in the charge column.  However, I guess you wouldn't 
need to use Dock Prep for that molecule if you already had a 
mol2-format file with the charges in it!

I hope this makes things clearer,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 22, 2007, at 10:55 AM, S Datta wrote:
> Hi
> I am trying to prep a ligand using chimera for
> docking. When I try to add charges, one error which is
> always present is "Atom whose IDATM type has no Sybyl
> type: #-99.-99:1 at CO(type: Co).
> At the end the reply log asks to check the total
> charge and spin multiplicity.
> When I manually change the total charge, after the
> Atom error briefly appears, Chimera either freezes
> (windows) or runs the program
> /../antechamber/exe/mopac.sh (in linux) infinitely.
> Could someone help me decipher what is going wrong ? I
> tried to change the input format of the ligand file
> from .pdb to .sy2 but that didnt help.
> thanks a lot
> SD

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