ADL: dont know what this means...???

Garrett M. Morris garrett at
Fri Mar 28 12:06:44 PDT 2008

Dear Namitha,

On 28 Mar, 2008, at 4:27 am, namita at wrote:

> Dear users
> Thanks for all the help given so far in helping me solve my issues.  
> To an
> extent I have succeeded in resolving many of my problems but again I  
> face
> many more...pls do help me this time again...
> I try to save in my receptor molecule (which is generated by  
> modeller) in
> pdbqt format. (Grid -> Macromolecule -> Choose)and then saves the  
> molecule
> in pdbqt. when I try opening this molecule again it asks me whether  
> i need
> to preserve charges or add gasteiger charges to it. Either i say no  
> or yes
> to that option it gives me a warning message like this :
> Non-integral charge on molecule:- -6.075
> correct 11 residues:
> HIS1 0.055
> GLN13 0.006
> LYS27 0.006
> TYR44 0.03
> PRO45 0.03
> GLU69 0.029
> PRO70 0.03
> ARG104 0.029
> PRO105 0.03
> ASN196 0.006
> PRO473 0.058
> Charges should be corrected in written output file!
> I would like to know how and where do i need to add these charges? Are
> they talking about the .pdbqt output file??


> Please help...any help would be greatly appreciated.

Sorry if this message from ADT is not clear.

One check ADT does on the macromolecule is to add up all the partial  
charges on each residue, to see if they sum to an integer.  The idea  
is that a side chain can be neutral or charged, but never carry a  
fractional electron...  This kind of error check can detect when there  
are missing atoms in a sidechain, something that is important in  
guaranteeing your molecular model is accurate.

These discrepancies are very small for each amino acid, so I would not  
worry about them too much.  I will talk with the ADT programmers about  
this.  You can actually edit the charges in the PDBQT file using a  
text editor.



> Thanks
> Namitha
> ________________________________________________
> --- ADL: AutoDock List  ---  
> ---

Dr Garrett M. Morris, MA (Oxon), DPhil (Oxon)

The Scripps Research Institute,       tel: (858) 784-2292
Dept. Molecular Biology,  MB-5,       fax: (858) 784-2860
10550  North Torrey Pines Road,       email: garrett at
La Jolla,  CA 92037-1000,  USA.

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