AMBER Archive (2008)

Subject: RE: AMBER: reg.building ions

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Fri Dec 12 2008 - 06:14:57 CST

Dear amber .,
actualy i took cobalt(III)hexammine from the nmr data
and i done the procedure given in tutorial 5
which explained for sustiva
but in my case it gives error
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Running: /home/balaji/AMBERHOME/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full

For atom[1]:Co, the best APS is not zero, exit

Running: /home/balaji/AMBERHOME/amber9/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

Total number of electrons: 87; net charge: 0
Number of electrons is odd: 87
Please check the total charge and your -nc flag
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
so ., the out put files are not generated
as like that
what i have to do
is it possible to solve it with amber
balaji.N
UOM

> Date: Fri, 12 Dec 2008 07:04:58 -0500
> From: case_at_biomaps.rutgers.edu
> To: amber_at_scripps.edu
> Subject: Re: AMBER: reg.building ions
>
> On Fri, Dec 12, 2008, balaji nagarajan wrote:
>
> > but wen i do for ions it gives error in -nc flag
>
> *What* did you do (exactly)? What was the error?
>
> [Usual comments here about how contributors to the Amber list are not
> mind-readers....]
>
> ...dac
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