Elaine's observation that Antechamber will not do a good job with metals is absolutely correct.  I would recommend editing your input file to put the colbalts into residues of their own.  This will allow Dock Prep to assign the proper charge to the metal (+2/+3) directly and run Antechamber on the remaining organic part of your ligand.  I intend to get Dock Prep to do this "metal separation" itself soon, but haven't gotten to it yet.

Also note that for large ligands (e.g. cobamamide) Antechamber can take many minutes to run on slower machines, so it's quite possible that what you thought was a "freeze" was in fact the charge calculation taking a while.  Try starting giving the calculation at least 10 minutes, and also checking if the "mopac" process is running, before deciding that the calculation is frozen.  If you do find a ligand that clearly freezes Chimera, send it to me and I'll look into the problem.

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        pett@cgl.ucsf.edu

                        http://www.cgl.ucsf.edu



On Jun 22, 2007, at 12:34 PM, Elaine Meng wrote:

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
-----
Elaine C. Meng, Ph.D.                          meng@cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

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@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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