ADL: dont know what this means...???
Garrett M. Morris
garrett at scripps.edu
Sun Mar 30 16:43:08 PDT 2008
Here is a quick update: the warning message refers to discrepancies,
and the version of ADT you have appears to have a more stringent
tolerance (later versions use 0.07). Read on for details:
On Mar 28, 2008, at 12:06 pm, Garrett M. Morris wrote:
> Dear Namitha,
> On 28 Mar, 2008, at 4:27 am, namita at ncbs.res.in 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
>> 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
>> 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!
NOTE: These numbers are the _discrepancies_ from the integer values,
not the absolute total charges.
>> I would like to know how and where do i need to add these charges?
>> 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
I spoke to Ruth Huey, and she informed me that:
> The tolerance was increased 2/23/07 to +/-0.07 in AutoDockTools/
> This last release which had .005, in principle, was 1.4.4 dated
> Releases dated 10/03/07 and later have the larger tolerance.
I would recommend you obtain the most recent version of ADT: is has
many new features as well as bug-fixes:
Version 1.5.0 is the latest "non-beta" version:
> You can actually edit the charges in the PDBQT file using a
> text editor.
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