[Dock-fans] How to get the charged mol for the ligand

Devleena Shivakumar devleena at scripps.edu
Fri Feb 1 17:51:02 PST 2008

Hi Thomas,

You have to give the total(formal) charge of the molecule to
CHIMERA/ANTECHAMBER for it to calculate the partial charge distribution
for your molecule.  Look at the molecule and use your chemical intuition
to judge the total charge. When you download ligands from databases, like
ZINC, the mol2 file comes with precalculated AMSOL charges. You can try
looking for your ligand in ZINC databse. Also see Eric's comment on your
ligand IMZ. 

>From my experience with amber score, am1-bcc gives better results compared
to gasteiger.

On Fri, 1 Feb 2008, Thomas Leonard wrote:

> Hi,
>   Thanks for your help.
>   How to check the total charge. can I fix the charge in chimera directly like +2,+1, 0 -1, -2. to choose from. (what is that.)
>   which is the best option am1bcc or gasteier?
>   Can I fix the charge arbitarily.
>   Thomas
> Devleena Shivakumar <devleena at scripps.edu> wrote:
>   Hi Thomas,
> Did you check the total charge? Is it 1? Does your ligand have all the
> hydrogens?
> Devleena
> On Wed, 30 Jan 2008, Thomas Leonard wrote:
> I could not get the charges for my molecule (ligand in x-crystal
> structure). how to do that?
> I am getting the following error message.
> I am using chimera to do these funtions.
> Running ANTECHAMBER command: C:\Program
> Files\Chimera\bin\antechamber\exe\antechamber -i
> c:\docume~1\thomas\locals~1\temp\tmpkzw4il\ante.in.mol2 -fi mol2
> -o c:\docume~1\thomas\locals~1\temp\tmpkzw4il\ante.out.mol2 -fo mol2 -c
> bcc -nc 1 -j 5 -s 2
> (IMZ)
> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe\bondtype -i
> (IMZ)
> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe\atomtype -i
> (IMZ) Total number of electrons: 351; net charge: 1
> (IMZ) INFO: Number of electrons is odd: 351
> (IMZ) Please check the total charge (-nc flag) and spin multiplicity
> (-m flag)
> Failure running ANTECHAMBER for residue IMZ
> Thomas
> ---------------------------------
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